I could have sworn I've already posted my answer. Hrm.
Generally, I prefer to adjust the setting to the game rather than the other way around. I also don't like to fiddle around with minor details, like individual class features, spells and feats (though I do develope my own).
But I made some big changes compare to Core:
-No sorcerer
-Free multiclassing. No xp penalties or barred classes.
-No alignment restrictions for base classes. Not even for paladins (LG is default, but exceptions exist). I also don't restrict PC alignments, but prefer to work out a social contract about what's acceptable at the table.
-Feats, skill ranks, new class features, arcane spells and non-PHB divine Spells need to be aquired in game. This isn't hard, nor a way to restrict what PC's can use, but I feel it binds PC's more into the game world and means stuff like mentors, wizard guilds, order, churches etc are more important. It also means can level mid session.
-I've slowed down advancement.
-I've used AP, but found they didn't do the job. I'm now working on my own Swashbuckling cards, mixed with neutral event card.
-I'm not really happy with how item creation and AC work (scales terribly and worst christmas tree offender).
I generally alow non-Core stuff, provided the player can convince me it makes sense in game, I own the book and it isn't a baseclass.