TL;DR VATS is disabled and perks that give bonus in VATS are modified to be useful again.

Also, if you like VATS, I'm completely fine with it as long as you just walk away.



Installation:

Not 100% sure that modifications to perks that player already acquired apply correctly.
Nothing I can do about it; it's engine problem.
Use console commends to remove and re-acquire modified perks to be certain.



Requirements:

Nuka World DLC
Far Harbor DLC



Complementary Mod:

Critical Hits Outside of VATS by NotSure700 - http://www.nexusmods.com/fallout4/mods/12653/?

HIGHLY RECOMMENDED! I did not modify perks that are already modified by this mod.



Full Change List:


Awareness
1Time slows down by 30% for 5 seconds when combat begins.
2Now time slows down by 50% for 8 seconds when combat begins.

Concentrated Fire
1You do 20% more damage to enemies with 30% or less health.
2Now you do 30% more damage to enemies with 40% or less health.
3Additionally, you do 50% more damage to enemies with 20% or less health.

Sniper
3Non-automatic, scoped rifles do 100% more limb damage.

Quick Hands
2Now you can reload all guns even faster. (50% faster; rank 1 is 35% faster)

Blitz
1You do 50% more melee weapon damage for 5 seconds after sprinting more than 2 seconds.
2Now you do 80% more melee weapon damage for 8 seconds after sprinting more than 1 second.

Gun-Fu
1Every time you switch to a pistol, rifle, or heavy weapon, you do 10% more damage with them for 10 seconds. The bonus stacks up to twice.
2Gun-Fu bonus stacks up to three times. Gun bashing does 50% more damage.
3Gun-Fu bonus stacks up to four times, and lasts 5 more seconds.

Grim Reaper's Sprint
1Any kill has a 15% chance to restore all Action Points. 
2Any kill now has a 25% chance to restore all Action Points.
3Any kill now has a 35% chance to restore all Action Points and reduce incoming damage by 50% for 5 seconds.

Penetrator
1You ignore 20% of a target's armor.
2Now you ignore 30% of a target's armor.

V.A.N.S.
1Track nearby human targets for 30 seconds.
2Track human and robotic targets further away for 30 seconds.

Critical Banker
1You have 5% chance of critical hit on enemies with full health.
2Now you have 10% chance of critical hit on enemies with full health.
3Now you have 15% chance of critical hit on enemies with full health.
4Now you have 15% chance of critical hit on enemies with 75% or more health.



Change Log:

1.1
- fixed Grim Reaper's Sprint rank 3 chance


Work In Progress:

- No clue how to change Mysterious Stranger perk; best possible implementation would be one in which the NPC spawns somewhere in the middle of a combat. I would have to do a lot more than tweaking perk entries for that, so currently it's untouched.

- Companion perks, legendary weapon mods, when I have time to look into them.

- Let me know if there is other game play elements that are VATS-dependent!



My Other Mods:

No VATS Overhaul: Disables VATS and modify VATS-dependent perks to be useful without VATS.
http://www.nexusmods.com/fallout4/mods/25428/?

Power Armor No Sneak: Makes sneaking extremely hard with power armors, especially when moving.
http://www.nexusmods.com/fallout4/mods/25051/?

Binary Pickpocket Overhaul: You can either pickpocket an item with 99% chance, or not at all, depending on your perk, agility, and the item's value. No more save & load bullshittery!
http://www.nexusmods.com/fallout4/mods/25123/?

Animated Chems - re-done Fix: Quick fix for FLipdeezy's Animated Chems - re-done mod
Original: http://www.nexusmods.com/fallout4/mods/13278/?
Fix: http://www.nexusmods.com/fallout4/mods/25094/?