Any form of shapechange, from alter self to polymorph; from core to the polymorphed subtype. Not only is this a redunant and convoluted mechanic, but the idea that these forms must be tied to the stats of existing creatures is just beyond pointless.
Fellow players with borderline personality disorder. This isn't really a general complaint, it's just big on my mind.
The inclusion of entirely new schools of gameplay design (like Book of Nine Swords, Magic of Incarnum, psionics, etc) with a system that was never built to include them, and because it includes them, necessitates that they be designed to work within the existing system somehow rather than simply behaving properly in an enclosed system. Players should not have the option of having a core fighter in the same group as a crusader, it's just not the same type of game for the two of them. 3rd party systems handle this in a way that blows WotC's method out of the water.
WotC owning whatever we post on their forums.
Poor software support across the board. We still don't have D&D Insider's promised system to facilitate digitally-based game displays, even though this is something that should have been implemented a decade ago. No company has yet to produce a viable character creation program that can compete with fan-created Excel sheets.
Alignment. The simple fact that we CAN argue about this means that it doesn't work very well. What's more, in a system that is not as shallow and fun-oriented as original D&D, the alignment concept fails to produce the amount of realism that 3.5 encourages. It's like having only different colors of the same car and thinking that's enough variety.
"What kind of car is that?"
"Oh, it's the red kind."
Half orcs. What a stupid idea for a race. If you really need a strong race to fill out your list, why not make one up or just go with orc? Instead we get bastards or children of violent rape popping into the game just so they can get a higher Str or to roleplay the "dumb" guy. I have a "final solution" for the half-breeds of the game. It rhymes with Mall-o-cost.
Arcane Spell Failure. It took them how long to build in a work-around for this limitation? Why not just prohibit casting in armor with which you aren't proficient and call it a day?
Multiclassing. This just does not work the way that it's supposed to, and the system doesn't need it to be an option at all.
Prestige classes. "Hey, let's make a class that has steep requirements so we can justify making it better than core classes."
"Won't people just plan every choice for their character around being the most perfectly qualified character possible for that class so they can get out of what will become a weaker class once you add PrC's?"
"umm.... but I already made 4, can't we keep em?"
Vancian spellcasting (that's spells-per-day for the newbs) in both prepared and spontaneous versions. Add to this: divine casters gaining spells differently than arcane casters (either make it automatic for both or none).
Inconsistancy in spell design. While I love the Spell Compendium, at some point someone should have pointed out that many of the spells are just attempts at making duplicates that fall into a different spell school, in order to allow for better Spell Focus utility for those who recognize that Evocation (among others) focus is pointless. The result: if you want to use a spell, from virtually any source, a good DM must look it over and consider it. The inconsistancy results in a necessitated automatic distrust.
Specific +2/+2 feats with their own entry, just because someone didn't want to say, "Pick two skills and you get a +2 to each."
Leadership feat. If you want to have followers you're required to build a character around this mechanic rather than simply roleplaying it out (also meaning that roleplaying has nothing to do with being a leader). If you want to work the system to get a cohort that allows you to never rely on your party, it's supported in the rules. Both are bad, and both are the result of this feat.
Crafting rules, the redundant Profession skill (which should be NPC-only anyway), an unlimited list of possible Knowledge and Perform skills, skill synergy bonuses, the ease of totally owning all skill checks once you're past a certain level, and the complete negation of the need for skilled characters thanks to certain spells and items.
All races live longer than humans? what the hell?