Notes:
Combat skills does NOT include Big Guns, if you have it enabled. Mainly because Deception exists and is too good to be ignored.
It is meant to be played along with a mod that allows for more Traits to be taken, such as Traits on Level up.
Sneak attack criticals bonuses from perks have been removed, due to me using "bNoSneakAttacksCriticals = 1" in lStewieAl's Tweaks and Engine Fixes.
If theres mod does changes to the same perk and you like the other one more, or this, just let the one you prefer over write the other.


Final perks turned traits. Death and new beginnings theme does fit better as a trait:


Ain't Like That Now:
Your Critical hit chance is no longer tied to your Luck, but Perception. You lose all Critical hit bonuses when your Perception drops below 5.
If your Luck goes above 5, you get the full penalty of -10 Critical hit chance, until it is back to 5 or lower.

Just Lucky I'm Alive:
Requires 2 Luck.
You lose 1 Luck. Your HP drops below 25%, you get the +4 Luck buff for 3 minutes.
With the various mod fixes for this Perk I couldn't remove the weird Luck buff, so thats the upside of the trait.

Thought you Died:   
Your Critical hit chance is 0. Enemies attacking you have 0 Critical hit chance as well.


Perks turned Traits, Complex:


Better Criticals: 
Critical damage increased by +25%. For every current point of Perception over 5 another +5%. Max +50%! You take -5 to Critical hit chance.

Finesse:      
Critical hit chance increased by +5. For every current point of Agility over 5 another +1%. Max +10! Critical hits do only 50% damage.

Demolitions Expert:  
Explosion damage increased by +15%. Explosion Splash Radius reduced by -15%.

Splash Damage:
Explosion damage increased by +15%. Explosion Splash Radius reduced by -15%.

Gunslinger:      
One handed firearms: +15% attack speed, +10% accuracy, +15% chance to hit in VATS.
Two handed firearms: -15% attack speed, -10% accuracy, -15% chance to hit in VATS.

Commando:     
Two handed firearms: +15% attack speed, +10% accuracy, +15% chance to hit in VATS.
One handed firearms: -15% attack speed, -10% accuracy, -15% chance to hit in VATS.

Old World Gourmet:  
Prewar Food Snacks heal +50% more. Scotch, Vodka and Wine give health as well. You have a +10% increased addiction chance.

Tribal Wisdom:  
You can eat insects. You gain +25% Poison resistance. You lose -25% Fire resistance.

Home on the Range:
You can sleep at campfires. You lose -25% Energy resistance.

Educated:   
Gain +2 Skill point every level. Lose -5 to every combat skill.


Perks turned Traits, Simple:


Bloody Mess: 
Removed the damage bonus, the classic.

Cannibal: 
Allows you to choose this option as a trait so you can be the cannibal character if you want right from the start. Have a nice meal.

Explorer: 
Because it didnt feel right as a perk you have to commit perkpoints for. You want to explore, go for it!

Friend of the Night:
Ew. Cateye Lite.


Trait balance adjustments:


Good Natured:
You take -3 to all combat skills, but you gain +2 to Charisma. Idea taken from S6S SPECIAL Base Game Perks Redux, but CHA stays a dump stat, unfortunate.

Heavy Handed:
Written in how much damage you gain (+25%) and how little critical damage you will deal (60%). Raised damage buff by 5 to 25.

Kamikaze:
Gain +10 AP, recover 15% more AP and run 10% faster but lose 25% energy resistance and 25% fire resistance, along with 15% damage resistance.
(Damage resistance loss is a vanilla feature but for some reason not mentioned in the perk.)

Hot Blooded:
10% more weapon degration. Gain 5% more damage. When health < 50%: 10% more attack speed and +3 to Critical hit chance, but lose 2 DT.

Skilled:
You gain +10 to all combat skills, this won't stack on taking this trait again. You gain 10% less experience and 2 less skill points every level.


Perk balance adjustments:


Cowboy:
Requirements: Level 16, Guns 45, Explosives 20, Melee weapons 35
Or Guns 65
Damage nerfed to +20%, Accuracy improved by +10%, AP costs reduced by 10%, VATS chance to hit increased by 10%
With Cowboy Weapons of course.

Grunt:
Requirements: Level 16, Guns 45, Explosives 35, Melee weapons 20
Or Guns 65
Damage nerfed to +20%, Accuracy improved by +5%, Movement speed while aiming +10%, AP costs reduced by 10%, VATS chance to hit increased by 5%
With Grunt Weapons of course.

Laser Commander:
Requirement: Level 22, Energy weapons 85
Damage +15%, Critical hit damage +10%, Critical hit chance +10%, AP costs reduced by 20%.
With Laser Weapons of course. Yup nerfed critical hit chance, this buffs it up again.

Plasma Spaz:
Requirement: Level 22, Energy weapons 85
Attack speed +15%, Critical hit damage +10%, Critical hit chance +5%, AP costs reduced by 20%, accuracy +10%.
With Plasma Weapons of course.

The Professional:
Requirements: Level 14, Sneak 40
Pistol, Revolvers and SMG's Critical hit chance increased by +5%. While undetected you gain 50% more to Critical hit chance and deal 25% more damage.

And Stay Back:
Requirements: Level 10, Guns 50
Base chance to knock back reduced to 5% per projectile. +1% for every point of Luck above 5, up to 10%, same as Vanilla.

Slayer:
Requirement: Level 20, Melee weapons 80 or Unarmed 80
Attack speed increased by 15%, increased by another 5% for every point in Agility above 5, up to 40%.

Ninja:
Requirements: Level 20, Sneak 80 and
  Melee weapons 80 or Unarmed 80
Critical hit chance increase of 15% for Unarmed and Melee weapons. Being undected gives you +50% damage and +50% critical hit damage.

Light Step:
Requirement: Level 8, Sneak 40, Agility 5, Perception 5
Chance to set off traps reduced to 50%.

In Shining Armor:
Requirements: Level 6, Repair 20, Science 40
"Fixed" the perk, by only giving its +5 DT on reflective armor (and +2 DT for reflective eyewear) against Laser weapons. Lowered Requirements because of that.

Pharmacist:
Chemist Perk name change. It feels like this name fits better.
3 ranks now. 1st rank unchanged: twice as long chem duration. 2nd rank: -20% addiction chance. 3rd rank: +20% healing from all sources


Just Requirements adjusted, Crafting Perks edition:


Junk Rounds:
Requirements: Level 2

Hand Loader:
Requirements: Level 6, Repair 35, Guns 35

Mad Bomber:
Requirements: Level 6, Explosives 25, Repair 25, Science 25

Vigilant Recycler:
Requirements: Level 6, Energy weapon 40, Science 40

Nuka Chemist:
Requirements: Level 12, Science 50, Survival 35. Survival because of the whole cooking aspect.


Just Requirements adjusted:

Heave, Ho!:     
Requirements: Level 2, Strength 5 and
  Melee weapons 30 or Explosives 30

Mister Sandman:
Requirements: Level 2, Sneak 50

Rapid Reload:
Requirements: Level 2, Agility 5 or Guns 30 or Energy Weapons 30 or Explosives 35. Because of the grenade rifles and Grenade Machineguns...
  (and because of Flamers and other Fire projectile weapons)

Terrifying Presence:     
Requirements: Level 2, Charisma 6 and
  Speech 50 or Barter 75 or Strength 8 or Perception 9

Entomologist:
Requirements: Level 2, Science 40, Survival 35

Computer Whiz:
Requirements: Level 6, Science 50

Infiltrator:
Requirements: Level 6, Lockpick 50

Pack Rat: 
Requirements: Level 8, Barter 70 or Survival 70

Walker Instinct:
Requirements: Level 10, Survival 50

Center of Mass:     
Requirements: Level 12, Guns 60 or Energy weapons 60

Pyromaniac:   
Requirements: Level 12, Explosives 60 or Energy weapons 60 or Unarmed 70 or Melee weapons 70.
Optional:   Script Runner that removes the +50% damage weapon damage, if you have Universal Pyromaniac Buff

Unstoppable Force:
Requirements: Level 12, Unarmed 60 or Melee weapons 60

Nerves of Steel:
Requirements: Level 12, Agility 5

Unstoppable Force:
Requirements: Level 12, Unarmed 60 or Melee weapons 60

Broad Daylight:
Requirements: Level 14, Sneak 70

Purifier:
Requirements: Level 14, Unarmed 75 or Melee weapons 75

Certified Tech:
Requirements: Level 20, Science 80, Repair 50
Also fixed the perk giving the bonus it promised.

Irradiated Beauty:
Requirements: Level 22, Survival 75, Endurance 7


Hidden Perk:
Here and Now. Weird, kinda useless and got fixed by other mods so I can't even think of something. Its just there to take space, now its hidden, F's in the chat.


My other Mods:

Script Runner Energy Weapon Rebalance
Script Runner Gun Rebalance
Script Runner Effect Enhancements 
Script Runner Miscellanous Weapon Buffs or Tweaks
Script Runner Weapon Skill Changes
Script Runner Recipe Changes
That one mod that does some effect integrations from The Frontier that I havent updated to Script Runner yet. Flame me on this until I do.
That one mod that does some effect compatability fixing for EVE that I havent updated to Script Runner yet. Flame me on that until I do.