A patch I made for my own game, that I thought I should probably upload after the time I've put into it.

Overhauls Perks, Skills, Traits and Ingestibles from these mods to interact well with one another:
Be Exceptional
You Are SPECIAL
Humble Perks
Better Locational Damage - Enhanced Perks
Start Me Up


Additional patches for:
Combined Arms
Damn Apocalypse
Tales of the Commonwealth

Ideally all plugins should be used, but you can choose individual ones if you'd like. All of them are flagged as ESL.


Plugins:

Alex - Perks Overhaul

This is mostly just a master for changes used in the other patches, but it also includes the following changes:

Locksmith Skill - Now increases lockpick sweetspot as well as allowing higher lock levels to be picked.
Strong Back 4 - Description now mentions it prevents leg damage when overencumbered in Hardcore.


Alex - Perks Overhaul - YAS

Added YAS Perks to Be Exceptional level up screen.
Added or changed skill and levels requirements to most perks.
Changed "Master" perks to be unlocked at level 100 of their respective skill, instead of when getting all 4 perks of it's type.
Moved Master Critical banker to rank 5 of Critical Banker instead of being unlocked when getting all 4 ranks of Critical Banker (same thing).
Turned Trader at Heart into Pillar of the Community rank 3, as they were overlapping anyway.
Removed Stonewall in favor of Be Exceptional's Bodybuilder.



Alex - Perks Overhaul - Humble Perks (Requires You Are SPECIAL)

Survival Skill now improves with Endurance.
Survival Skill now increases healing from food.
Changed several perks to be unlocked at higher levels, most where unlocked at level 0.
Added other skill and SPECIAL requirement to most perks, from needing only Survival.
Removed HP's Parkour Enthusiast/Master in favor of You Are Special's Acrobatic.
Removed YAS's In Raider's Armor, Stay Frosty and Sharpshooter, in favor of HP's Lowlife, Stay Frosty and Sharpshooter.
Changed Low Life effect to be more in line with You Are Special perks of the same type.
Fixed some perks to display correctly in the level up screen when checking all ranks.
Added Survival Skill requirements to a few BE and YAS perks.



Alex - Perks Overhaul - BLD - Better Perks Enhanced
Carried over changes to perks from Be Exceptional when using Skills instead.

Perks changed back to their Be Exceptional version:

Action Boy/Action Girl
Ninja
Aquaboy/Aquagirl


Perks using Better Perks - Enhanced versions:

Chem Resistant (added rank 2 back)
Night Person
Lone Wanderer (added rank 4 back)
Steady Aim


Alex - Perks Overhaul - WI (Requires Humble Perks and You Are SPECIAL)

Changed most skill magazines to increase their respective skill temporarily.
Added HP's Thoughtful Reader effect to all skill magazines (They give 20XP instead of 100XP).
Kept Be Exceptional changes in certain perks, to make sure they aren't overridden.
Added New Vegas Comprehension perk (double skill gains from magazines) as rank 2 of Thoughtful Reader.


Alex - Perks Overhaul - Start Me Up (Requires You Are SPECIAL)

Added Start Me Up Traits to You Are SPECIAL traits list.
Don't pick any traits in Start Me Up menu.

Alex - Perks Overhaul - Clothing & Armor (Requires Far Harbor, Nuka World and Humble Perks)
Added skill bonuses to some pieces of clothing and armor.


Alex - Perks Overhaul - Optional - Slower Leveling
With skills on top of perks decreases the need to level up as often.


Alex - Perks Overhaul - Optional - Skill Points Rebalanced
Even with skills on top of perks, the player still needs to level up SPECIAL more often than before, so skill points per level are reduced:

Base skill points per level reduced to 8 from 10.
Intelligence increases skill points per level by 1 every 2 points, instead of 1 to 1.
Educated perk increases skill points by 2 instead of 4.
Tagged skill increases by 12 instead of 15.


Alex - Perks Overhaul - Optional Changes

My own personal changes to different perks. These I use on my own playthroughs.

Carried over Barter changes from Damn Apocalypse.
Changes Unbreakable to Master Locksmith, it now just increases lockpick sweetspot instead of making bobby pins unbreakable.
Removed rank 3 and 4 from Fortune Finder and Scrounger, adding rank 4 effects to rank 2, but unlocking them at a much higher level.
Quick Hands now improves reloading speed at every rank, on top of the VATS and AP bonuses rank 2 and 3 provide.
Removed HP's Special Tactics and Recon Unit, since I use mods that allow companions to sneak by default.
Added 10% XP gain bonus to Lone Wanderer rank 4.



Alex - Weapons Accuracy - Overhaul
With Better Locational Damage I felt that investing in weapon skills wasn't very useful, since weapons do much more damage, one shot most enemies with easily acquired weapons, and you have incredible accuracy without spending a single point in any weapon skill.

Accuracy is drastically reduced at low skill levels, but improves a lot at higher skill levels.
Accuracy increase is lessened for Heavy Weapons skill, but Strength now buffs that as well.
Vertibird Minigun has not been nerfed, or you might get stuck in the obligatory turret sections if you didn't level up Heavy Weapons.
Personal Vertibird mod uses its own Minigun, which will be affected by the nerf.

Optional Patches:
Tales of the Commonwealth Alex - Perks Overhaul - 3DNPC - Patch
Combined Arms Alex - Perks Overhaul - CA - Patch
Player Comments Alex - Weapons Accuracy - Overhaul - Player Comments


You should order these plugins like this:

Mojave Imports
You Are SPECIAL
Be Exceptional
Humble Perks
Better Perks Enhanced
Start Me Up

Alex - Perks Overhaul
Alex - Perks Overhaul - YAS
Alex - Perks Overhaul - Humble Perks
Alex - Perks Overhaul - BLD - Better Perks Enhanced
Alex - Perks Overhaul - WI
Alex - Perks Overhaul - Start Me Up
Alex - Perks Overhaul - Clothing & Armor

Alex - Perks Overhaul - Optional - Slower Leveling
Alex - Perks Overhaul - Optional - Skill Points Rebalanced
Alex - Perks Overhaul - Optional Changes

Alex - Weapons Accuracy - Overhaul
Alex - Weapons Accuracy - Overhaul - Player Comments

Alex - Perks Overhaul - 3DNPC - Patch
Alex - Perks Overhaul - CA - Patch