In campaigns I run, absolutley Ill mess with something to fit the setting flavor.
Some examples of my Chronicles of the Arcanist tweaks:
Soulknives (with some abilitiy tweaks) are an Incarnum class and not psionic.
Paladins can be any good or any evil (the the abilities appropriately tweaked for good or evil) and giving the players the option of not having the pokemount and instead having an item familiar that is usable only for weapons. (good ole 2e paladin swords!)
Rangers get no spellcasting, instead they get a full progression animal companion.
Fighters I give an option of every odd-numbered fighter level after 3rd if they would get at least 5 skill points at the time of leveling up they can choose to spend a those skill points on a bonus fighter feat.
I have found these work out pretty good.
Some examples of my Chronicles of the Arcanist tweaks:
Soulknives (with some abilitiy tweaks) are an Incarnum class and not psionic.
Paladins can be any good or any evil (the the abilities appropriately tweaked for good or evil) and giving the players the option of not having the pokemount and instead having an item familiar that is usable only for weapons. (good ole 2e paladin swords!)
Rangers get no spellcasting, instead they get a full progression animal companion.
Fighters I give an option of every odd-numbered fighter level after 3rd if they would get at least 5 skill points at the time of leveling up they can choose to spend a those skill points on a bonus fighter feat.
I have found these work out pretty good.