Oh my. So much to choose. It's like being in an inverse candy store.
I'd nerf AoO straightaway as being the single most pointless contentious game-stalling mechanic ever invented (cue wise-ass posts saying "I understand it, read the rules, what's not to understand", yadda yadda. I understand it. I don't like it. End of.). Take that away and all the feats, spells, etc which uses it's meta-gameness, and you'll have a better, thinner rulebook, immediately.
After that, I'd get rid of the whole LA/ECL/CR debacle. Just use Hit Dice as a relative measure of power as nature intended, and be done with it. Let the DM decide what's a suitable challenge for the party, or what's ok as a player race. As a DM I want rulebooks which empower me to make the right choices, not a set of rules and abbreviations which take power away from me. That'll simplify assigning XP too, which is also a Very Good Thing.
That's pretty much it. I don't mind PrCs (I've have very few players want to use one, so it's a non-issue), and the magic system(s) works well enough for me. The grappling rules were spawned from the Abyss itself, but there's nothing a little House-ruling/common sense can't fix.
Yeh. AoO and LA/ECL/CR. Die, die, die.