A comprehensive enhancement pack for Fallout 4, which focuses on fixing gameplay bugs & inconsistencies, massive balance changes across the board, and rebalancing all valid modes of gameplay: This mod is not targeted towards Survival mode; while it should work fine, the balance may not be quite right. Requires All DLC & The Unofficial Patch. 

General Changes:
Limbs no longer auto-heal after combat.
Companions no longer have access to an unlimited ammo weapon. Additionally, the Player only benefits from a companion perk if they are currently traveling with that companion.
To give purpose to the many time based mechanics through Fallout 4 (Such as merchants restocking every 2 days), the Player now gets weaker every 15 days as a result of their botched cryogenic stasis, taking a -1 to their highest S.P.E.C.I.A.L. Fast Travel speed has been multiplied by 4 to complement this.
Failing a Terminal Hack will now lock you out for 3 hours.
Charisma checks are no longer random: instead you need 5/10/15 Charisma to pass the different checks. Pick-pocketing likewise has become much less random, with most chances being either 0% or 100%, although it is possible for items to occasionally fall in between. 
"Guide to Diamond City" now gives +2% movement speed.
"The Unstoppables" now gives +2 Damage & Energy Resistance at every rank, instead of miss chance.
Weapon Bobbleheads now give +3% damage, instead of +25% critical damage.
The Explosives Bobblehead now gives +5% damage, instead of +15%.
The Energy Weapons Bobblehad & Tesla Magazines now apply to the Flamer & Cryolator.
The chance of Legendary enemies spawning is the same regardless of your difficulty (Identical to old Very Hard/Survival spawn rate.)
Destroyer of Acadia has been significantly nerfed. Protector of Acadia actually works now, but is nerfed compared to it's intended effect.

Consumables:
Healing from food is dramatically slowed down, similar to survival.
Healing from Stimpaks has been halved, but takes place VERY quickly (1 second). RadAway has also been halved. It now costs 100 caps to get Rads removed at a doctor. Curing addiction has also been increased to costing 125 caps.
Purified Water has been reduced from 40 healing to 30.
Most recipes using dirty water now use purified water.
Bobby Pins, Stimpaks, & RadAway appear 50% less often in loot tables.
Medkits have a 50% chance of being empty. This in addition to the fact that Stimpaks & RadAway appear less often in Medkits as well.
Refreshing Beverage is no longer craftable. Addictol is now craftable at the Chemistry Station using almost the exact same recipe, using 1 less RadAway and 1 more Stimpak.
Merchants no longer sell cryo cells or cannonballs. Instead, both of these items can be crafted at a Chemistry Station.
Drugs now require the Chemist perk to craft. See the Chemist perk under Intelligence for more information.
Overdrive now gives +50% critical damage rather than a 25% chance to randomly crit.
Combined drugs such as Psychojet, now give a smaller change to be addicted to either component drug; previously, all of these drugs only had a chance of getting you addicted to one of the component drugs, in most cases, Jet.
Daddy-O no longer reduces your Charisma, and grants the V.A.N.S. perk as well.
Day Tripper now gives +6 Luck.
X-Cell's duration has been increased from 2 minutes to 5 minutes.
The Deathclaw Egg Omelette does not have a healing effect, but regenerates 1% of your Health/20 seconds for 2 hours now. Regeneration works in combat now.
Radscorpion Egg Omelette gives +25 Damage resistance for 1 hour, instead of curing addiction. (v2)
Yao Guai Roast increases melee damage like it claimed to, instead of doing nothing. (v2)

Combat Changes:
Sneak Attack bonuses have been lowered from x2/ranged and x3/melee to x1/ranged and x2/melee. Perks which increase sneak attack damage remain unchanged however.
NPCs no longer become less aggressive in groups.
V.A.T.S. targetting phase moves 4x slower now, but the player no longer has any damage reduction during V.A.T.S.
Legendary monsters now have their offensive bonuses on from the beginning, and regenerate in combat, but do not instantly recover all their health when dropped to below half. Additionally, the increased Radiation damage effect, which ghouls and some other creatures had, now works (Was not increasing their Radiation damage in the base game.)
Enemy compass base range has been removed, but the range gain from Perception is unchanged.
Mines are no longer disarm-able without Sneak 4 because they go off VERY fast now.
It now consumes 3x more Action Points to hold your breath while aiming with a scope.
There are 5 levels of sounds in Fallout 4; Silent, Quiet, Normal, Loud, & Very Loud. Silent noise is unchanged, quiet and normal sounds are slightly louder for NPCs to hear, loud and very loud sounds have been increased tremendously, guaranteeing that these sounds will draw nearby NPCs to your position.
Radiation damage for creatures has been standardized to always be an instant 1 hit effect, which makes it harder to mitigate it using small amounts of Radiation resistance. Ghouls for instance inflicted a 5 second Radiation DoT with every attack, which made it very easy to mitigate. Now all that juicy radiation is applied instantly. This is how it worked for most enemies in Fallout 4, with the only notable exceptions being ghouls & bloatflys.
Flare Guns, Artillery Smoke Grenades, & Vertibird Smoke Grenades now have no weight.
NPCs will use Stimpaks sooner to compensate for their reduced healing.
NPCs are more aggressive about flanking, and are also less likely to leave their cover unless flanking. (v2)
Slight bonuses to the player's sneaking ability while indoors has been removed. NPCs are no longer less aggressive while looking for the player when indoors. It's harder to return to stealth after attacking an NPC now. (v2)

Weapon Changes:
Molotov cocktails now do 90 energy damage over 3 seconds.
Baseball grenades now explode on impact, but travel 50% faster and farther than normal grenades. Use 2 cork & 1 leather to craft instead of 1 baseball (Which gives exactly 2 cork & 1 leather.)
Minigun damage has been increased by 25%.
Flamer upgrades no longer reduce its range. Additionally, the Napalm tank no longer increases damage; instead it adds a 3 second DoT similar to Incendiary onto the weapon.
The Cryolator's base damage has been improved, and no longer claims to have a longer range than it actually does; the cryogenic capsules upgrade now requires Science 4, and only gives +8 ballistic damage.
All underslung heavy weapons, like the Minigun, Flamer, Broadsider, etc., no longer have a reduced cone of fire while crouching, and their cone of fire is only reduced by 20% while aiming (Standard is 60%. Miniguns have always had the latter weakness.)
The Broadsider's damage has been increased to 200.
Rockets,Fatmen, and the Broadsider no longer have projectile damage. This could lead to some confusion where effects like the Explosives Bobblehead didn't increase the damage as much as one might expect. 
The submachine gun's damage has been increased from 10 to 23, but it's cone of fire is only reduced by 20% while aiming.
Rocket Launchers and Fat Men are now more inaccurate when fired while moving.
Mininukes now deal 100 Radiation damage, and leave a radiation hazard behind, similar to a Nuka-grenade.
Bleeding effects now check against Damage resistance, but have been doubled in intensity.
The Harpoon Gun's bleeding enhancement now does 3x as much damage as other bleeding enhancements (60 Ballistic damage/5 seconds.)
Partystarter now has Stalker's instead of Assassin's, because Assassin's didn't do anything for explosive damage. Rocket launchers will no longer spawn with effects that don't affect explosive damage.
Many of the melee enhancements have less random effects, and more reliable boosts.
The armor penetration on melee weapons has been increased from 15% to 40% (Which is what ranged weapons had.)
The lead-lining enhancement on the boxing glove now has armor penetration.
The Deathclaw Gauntlet enhancement now does additional damage and causes bleeding, instead of having a chance to disarm.
The Burning Effect on laser Weapons (Beta Wave Tuner, Gamma Wave Emitter, Boosted Gamma Wave Emitter) now deal radiation damage instead of a burning effect.
Modifications that add DoTs such as serrated now say exactly how much, e.g. instead of "targets bleed", it says "+20 Ballistic damage/5 seconds."
Gamma guns and their unique variants no longer do direct radiation damage, which could deal massive damage to enemies who were supposed to be immune to radiation. The standard radiation poisoning, which worked as intended, is still present.
The legendary effects have been rebalanced. A few examples include:
Wounding now checks against Damage resistance, but its damage has been increased from 25 to 35.
Incendiary & Poisoner's now stack, similar to Wounding.
Hitman's has been increased to +25% damage while aiming, Mighty/Powerful has been nerfed to +20% damage.
Two-Shot recoil has been increased.
Nocturnal no longer does less damage during the day.
Explosive can no longer benefit from both Heavy Gunner & Demolition Expert.
Plasma infused's damage has been increased from 10 to 20.
Stalker's now increases your out of combat V.A.T.S. accuracy by 50%, and doesn't cost additional action points to use.


Armor Changes:
Instead of Armor saying Medium/Heavy, which is overwritten by modifications, they now say B or C, which isn't overwritten when modifications are added. E.g., Heavy Leather Armor becomes Leather Armor C. When you add a studded modification to it, it becomes Studded Leather Armor C, instead of just Studded Leather Armor.
Piezonucleic Power Armor now gives +25% Action Point Regeneration, but the Radiation resistance it gives has been halved. The old effect did not work, and did nothing. Additionally, the Power Armor piece is always a T-51 model, instead of being random.
Hazmat suits & Power Armor used to have a hidden perk that reduced all radiation damage you took by an additional 90%, on top of the massive radiation resistance. This has been removed.
The on-hit effects from Far Harbor, like Incendiary, have been buffed.
Most of the miscellaneous modifications, like Brawling, now say exactly what they do, e.g. "+10% Unarmed damage", instead of "Increased unarmed damage."
Grognak's Torso now gives +4 Strength. The increased melee damage effect it claimed to have didn't work.
Dirty clothing is now inferior to clean clothing, e.g. a dirty suit only provides +1 Charisma.
Sunglasses now give +5 Energy resistance instead of +1 Perception.
Bandannas now give +1 Radiation resistance.
Dog armor & collars now give small amounts of Damage resistance. 

Settlement Changes:
Plants in settlements are no longer harvestable by the player. Wild plants now give food that can be used to plant crops in settlements.
Turrets & Power generators have been rebalanced to provide more defense/caps spent as you build higher tier turrets.
Settlers are only capable of providing 4 defense now.
The robotics workbench now requires Robotics Expert 1 to build.
T2 shops, with the exception of the clinic, now require Bottlecap collector 1 to build.
The first tier of the clinic does not require Medic. The 2nd and 3rd tiers require Medic 1 & Medic 2 respectively.
The Nuka-mixer stations require Local Leader 2 to build.
Logic Gates now only require 1 steel to build.
Traps have been rebalanced so that they're actually useful. They're generally cheaper than turrets for defense/caps spent at first, but still require repairs whenever they're activated.
The various Vault items which provided a permanent S.P.E.C.I.A.L. boost, like the weight bench or pommel horse, no longer do.
Building your settlers mattresses instead of sleeping bags will increase their happiness by 1. Building them beds instead will increase their happiness by 2. The bed from the Vault DLC no longer uses less resources than the other beds.
Smaller shipments are now less effective in terms of resources/caps spent compared to larger shipments.
Artillery emplacements only provide 4 defense. (v2)
The workbench caps have been greatly increased: Food has gone from 10 + 1/settler -> 0+5/settler. Water has gone from 5 + 1/4settlers -> 0+5/settler. The scavenger cap has been increased from 100 + 5/settler -> 0+100/settler. (v2)
The chance of attack per day has been changed. It no longer has a 2% minimum chance of occurring each day, so it is possible to ensure that a settlement will not be attacked. The chance a settlement will be attacked has been changed to 0.5%*(Food + Water Production)-0.5%*(Defense). So if you have as much defense as Food + Water production, your settlement will not be attacked; however letting your resource production outpace your defense puts your settlements at much higher risk of attack. Finally, settlements no longer have a 7 day cooldown on how often they can be attacked. (v2)
Vendors are no longer capped to 50 bottlecaps/day. Now they can produce up to 999 bottlecaps/day. (v2)
Industrial Water Purifiers only produce 20 water, require Science 2, but do not require screws to build. (v2)
Unemployed settlers will no longer produce junk. Settlers assigned to scavenging stations still produce 2 pieces of junk every day. (v2)
The Decontamination Arch now requires Medic 4 & Science 4 to build. (v2)
Unhappy settlers will produce even less. As settlers became less happy, they approached 20% production. Now they approach 0% production as they become less and less happy. (v2)


Perk Changes:
Strength:
Basher: Now requires 1 Strength. Every rank gives +25% bashing damage and 10% chance to knock opponents down instead of old benefits.
Big Leagues: Every rank gives +20% melee damage & +15% limb damage instead of old benefits.
Iron Fist: Now requires 5 Strength. Every rank gives +20% damage & allows criticals in V.A.T.S. to paralyze for 2 more seconds instead of old benefits.
Steady Aim: Now reduces the Cone of Fire by 20% every rank, regardless of if you fire from the hip or not.
Heavy Gunner: Now requires 8 Strength. Every rank gives +20% damage, and reduces the Cone of Fire on heavy weapons by 10% instead of old benefits. No longer stacks with Demolition Expert.
Pain Train: The second rank makes all your melee attacks hit multiple targets while in Power Armor, similar to old Big Leagues rank 4. The damage from running into people with Pain Train has been doubled, but is now subject to Damage Resistance, where before it was unchecked damage.

Perception: 
Awareness: Now requires 1 Perception. The 2nd rank gives +20% damage in V.A.T.S.
Gunslinger: Now requires 2 Perception. Every rank gives +20% damage and a 4% chance to disarm enemies instead of old benefits.
Rifleman: Now require 3 Perception. Every rank gives +20% damage, and no additional benefit, since non-automatic rifles are the best weapons group.
Demolition Expert: No longer stacks with Heavy Gunner. Rank 4 increases explosion radius by an additional 25% (for a total of 50%) instead of giving you double damage if you manually shoot your grenades/mines in V.A.T.S.
Night Person: Now gives +2/+4 Perception & Agility for the first 2 ranks. Rank 3 makes you harder to detect while sneaking & night vision.
Refractor: Now gives +10/+22/+36/+52/+70 Energy Resistance.
Sniper: Every rank increases your scoped stability by 50%, and increases the damage you deal with scoped weapons, while aiming, against targets at least 30 meters away, by 20%.
Concentrated Fire: Now gives +6/+12/+18% damage & accuracy at every rank.

Endurance:
Toughness: Now gives +8/+18/+30/+44/+60 Damage Resistance.
Lead Belly: The first rank is as strong as the old 2nd rank. The 2nd rank gives immunity to ingesting radiation like the old third rank.
Life Giver: Now gives +20/+50/+90 Health. Regeneration has been removed (Regeneration being this early in the tree invalidated Lead Belly & Cannibal.)
Aquaboy: Rank 2 now allows you to regenerate 1% of your Health every second while submerged. Regeneration now works in combat.
Rad Resistant:  Now gives +15/+35/+60/+90 Radiation Resistance.
Cannibal: Now heals 50/100 Health (Over 100 seconds) & gives a +1/+2 Endurance buff for 5 minutes. Used to heal 25/50.
Ghoulish: Now removes Radiation (Think old 4th rank) at a rate of 1/3/6/10 rads per 5 seconds. (4th rank used to remove 8 rads/5 seconds.)
Solar Powered: Now gives +2/+4 Strength & Endurance for the first 2 ranks. The 3rd rank causes you to regenerate 2% of your Health every second. Works in combat now.

Charisma
Lady Killer/Black Widow: Now gives +2/+4/+6 Charisma for the purposes of passing persuasion checks in dialogue and for successfully pacifying enemies using Intimidation (more on that further down.) Previously, these perks actually made pacifying HARDER because of a little confusion on Bethesda's part with < signs.
Attack Dog: Now gives you +10/20/30/40% accuracy in V.A.T.S. while Dogmeat is holding someone, and increases his limb damage by 25/50/75/100%.
Animal Friend: Chance of success has been changed to 5%*Charisma. Additionally, putting away your weapon will not cancel the pacifying effect. Finally, Animal Friend now works against higher level enemies, and only has 2 ranks, skipping the middle rank where you can incite but not command animals.
Inspirational: 3rd rank now gives +50 Health in addition to Carry Weight.
Wasteland Whisperer: Chance of success has been changed to 5%*Charisma. Additionally, putting away your weapon will not cancel the pacifying effect.
Intimidation: Chance of success has been changed to 5%*Charisma. Additionally, putting away your weapon will not cancel the pacifying effect.

Intelligence:
V.A.N.S.: Rank 2 now available at level 20.
Medic: Now gives +50/100/150/200% Blood pack, Stimpak, & RadAway effectiveness.
Chemist: Duration bonus has been halved. However, you need Chemist to make chems now, as follows: Rank 1 allows you to make basic chems, including Jet, Buffout, Psycho, Med-X, Mentats, etc. Rank 2 allows you to combine chems to make Buffjet, Psychojet, etc. Rank 3 allows you to make "designer chems", such as Grape Mentats, Jet Fuel, Overdrive, etc. Rank 4 allows you to make advanced chems, like Calmex, Daytripper. X-Cell, etc. Many of these advanced chems have been buffed to make them feel like big deal t4 chems.
Nerd Rage: Effects have been better spaced out. The damage resistance doesn't kick in until rank 2, and the only effect gained at rank 3 is the on-kill heal, which has been doubled from 50 to 100.

Agility:
Pickpocket: Now requires 1 Agility. Numbers have been tweaked to accommodate the change where pickpocketing is very rarely random now.
Commando: Every rank now gives +20% damage and a 2% chance to stagger.
Mister Sandman: Sneak attack bonus has been increased to match Ninja, and now gives Sneak attack damage to Stealth Blades as well.
Moving Target: Now gives 20/40/60% Ballistic & Energy damage reduction while sprinting.
Ninja: Melee weapons no longer gain the huge boost in damage at rank 3.
Quick Hands: Both ranks 1 and 2 give 35/70% faster reloading and 50/100% less Action Points to reload in V.A.T.S. Rank 3 reduces V.A.T.S. Action point cost for all guns by 10%.
Blitz: Rank 2 no longer gives a damage bonus.
Gun-Fu: Rank 3 now gives +90% damage instead of automatic criticals.

Luck:
Scrapper Loot tables have been changed. Is no longer leveled, and is no longer biased towards certain ammo types, such as .50 cal.
Mysterious Stranger: Now has a 25/50/75/100% chance to execute your target at the end of V.A.T.S. if he is below 30% Health. (Almost identical to how it worked before, it's simply transparent as to how it works now.) No longer gives crits.
Idiot Savant: Is no longer random. Now gives +30/+70/120% experience on kills, persuasion checks, and discovering locations, with penalties scaling off your Intelligence. Turns off if you have 10 or more Intelligence.
Critical Banker: Rank 3 no longer allows you to generate additional crits by banking.
Grim Reaper's Sprint: Now gives a 15/30/45% chance to fill your Action Points, but can no longer give crits.
Four Leaf Clover: Now gives +15/30/45/60% more crit charge, instead of being random.
Ricochet: Now has a 3/6/9-12/24/36%, increasing as your health gets lower, chance to activate, dealing double damage to the enemy. No longer rewards additional crits.

Note: More changes than this have been made; this merely covers the most significant ones.