1. Pointless prereq feats. The best feats in the game have hardly any prerequisites, while basic combat styles require a crapton of tax feats.
2. "+1" magic items. Ugly, flavourless, and could functionally be replaced by just trimming down the numbers in monster statblocks. Magic items need cool effects, and just increasing the digit attached to it has no coolness whatsoever.
3. Multiclass penalties and favoured classes. They don't do what they are intended for, are pretty much worthless in every way.
4. Aid, Bless, and similar buff spells. Keeping track of miscellaneous minor bonuses is tedious, and getting +1 to attack doesn't make anything more fun, nor are other narrow miscellaneous bonus.
5. The skill system's "max ranks is class level+3, half that for cross-class skills, a point spent on a cross-class skill buys ½ rank, multiply skill points by 4 on first level"
aarg too complicated. I'd reduce the skill DCs a bit and just make max ranks equal to character level for class skills and four for cross-class. That way class skills remain important (since I feel they help define the classes well), but you don't have to deal with any math.
6. Feats that just give universal passive bonuses to your numbers (for example: improved toughness, improved initiative, iron will). They make for boring characters, adding these bonuses all over the character sheet is tedious, and I don't feel they make the game any better with their presence.
7. "All base classes are 20 level." I think that the need to stretch these out so far is one of the causes of balance issues. Multiclassing can be a normal and expected thing that is encouraged by the core rules, especially when a class just plain sucks after a certain level. If it ran out of decent class features, then it probably should just be cut off and the player moves on to another class.
8. Sucky feats. Making them suck less would definitely be an improvement.
9. Dead levels and boring classes. I wouldn't go the PF route of clogging the classes with a ton of minor features, but often major features are perfectly justified in these classes. Spellcasters are an exception, since so much of what they do is attached to their spell list and slots, but even casters could use some features here and there.
10. Iterative attacks. Keeping track of what bonuses each attack is using. I'd use a slower gain of attacks but all at the highest bonus, so you can roll them at the same time without paying attention to which die is which.
I'm stretching it a bit now, but if I try I can keep going for quite a bit. Indeed, give a dude enough time and he'll make a whole new edition of D&D, step by step!