Grouping skills seems to me as an unneccessary change which would made all chars the same
Tagging is ok if you ask me. Perks every 2 lvls and splitting the strong ones is a good change imo.
AC hit reduction is fine, but 60% is too much. 30% would be enough
Perks:
Polished armour: Kinda weak toughness.
Ghoulification/Fast Shot: Overpowered
Removing crit burst is just plain stupid, better to balance it than to remove it.
Not splitting bullets and using linear function (dmg/range) would make many guns overpowered. You need different function to describe damage distribution
Only pistols can do eye shots is another unjustful simplification of combat system. I dont see any reason why to increase crit dmg
Stamina is very good suggestion, would make fights last longer, something inbetween of 2238 and Requiem. But Im afraid, this change would have to be hardcoded to the engine.