Thoughts on perks to fix:
Bonus HtH/Ranged Damage: bonuses should be triple or something. (also Per says HtH bonus gets applied to max damage and should apply to min AND max).
Silent Death: triple or quadruple damage (usually only get this off once per combat anyway)
Mysterious Stranger: Stranger should appear in ALL random encounters
Adrenaline Rush: +2 ST and +2 EN? might be a little much though
Comprehension: should also raise the maximum skill level able to be gained by reading books
Demolition Expert: bonus should be applied to grenades (if it isnt) and should be super humungous
(or also merge with Light Step for the hell of it)
Empathy: +20 to speech as well?
Earlier Sequence: 1 rank instead of 3, but make the bonus much bigger (if possible would be cool if it could give you an Extra extra bonus round).
Ghost +40 to sneak instead of +20 (and/or merge with Night Vision)
Silent Running: +20 to sneak in addition to being able to run while sneaking.
Educated: 1 rank instead of 3 but gain 5 extra skill points per level rather than 2 (and maybe merge with comprehension?)
Smooth talker: +2 pretend IN but only one rank instead of 3
Quick Recovery/Stonewall = merge into one perk
Cautious nature/pathfinder: merge into one perk
Healer/faster healing: merge into one perk