Severe overuse of magic items in 3e! Not only does this turn you into a Christmas tree and force you to account gold way too much*, but it also makes designing NPCs, as well as PCs above 1st-level, a brutal PitA.
It also seriously weakens classed NPCs that aren't spellcasters (while NPC spellcasters would love more gear, at least they can dish out all their spells during and right before an encounter, often making them overpowered).
* This falls in squarely with the amount of treasure you have to hand out in 3e. Even if you hand out the massive amounts of treasure "correctly" in 3e, a lot of it's value is lost when it gets sold. Most of the time you find treasure that's not worth it. (Ooh... I have a +2 battleaxe, so I guess this +1 shortspear is kind of pointless.) This tends to hurt non-spellcasting PCs, too, since even with the huge amount of incoming $ they're not actually getting enough.
It starts to resemble Diablo or Angband at lower levels... you don't run home because you're hurt, you run home
because you can't carry more gear! You don't have to do this at higher level because everyone has their own
portable hole.
From all of the clearly 3e books I read (eg Erevis Cale Trilogy, part 1, where they specifically mention the term
shadow adept) the heroes are
not covered in magic items. In fact, an evil mage is
surprised when his obviously high-level minions have magic on them... turns out they've each got a solitary magic ring!
In 2e, treasure used to be a reward, but in 3e it's a necessity! I don't dare hand out extra treasure as a reward, since that will just cause balance problems down the road
And handing out less treasure, which I'd like to do, also causes game balance problems.
Mages go from hero to zero... without spells they're so weak and pathetic, and of course you
will run out of spells sometime. Mage defensive spells are often all-or-nothing, with
greater invisibility being the worst offender. I often spread beaded or gauze curtains around my castles to keep invisible mages... well, somewhat visible. If a mage has that spell up they're nearly unstoppable, especially in the open when the mage is flying and using
nondetection (the better to avoid
potions of see invisibility that smart fighters carry) the wizard totally dominates (very bad with an NPC mage)... on the other hand, a lot of mage defenses just suck.
Fire shield and any attempt to boost AC past the low levels without changing your shape are usually too weak.
Mirror image is, IMO, the best all-round defense spell a wizard can get - not too strong, not too weak either. I'd also love to see mages get some spells that defend themselves against magic (say, a balanced version of the elven
mantle spell).
Class skills (D20 Modern to the rescue again) are often ... lame. Fighters don't get Spot, for instance, so past a few levels there's no point of taking the skill, since the rogue is pretty much guaranteed to get past you no matter what you roll. (In Modern, several occupations can give you Listen and Spot as class skills.)
Last but not least, I hate how so much of your AC is based on magic items. Even if you're a rogue your AC probably rises more because of magic items (including Dex-boosting items) than because of your own character abilities. Many other characters simply never learn to defend themselves. Only the monk breaks the trend... but I dislike it for so many other reasons (eg it's lame, lame, lame, IMO). The game system also makes lightly-armored fighters very weak at low levels, and often overpowered at high levels.
(D20 Modern solves this problem, at least partially, by making sure characters can defend themselves and by making armor feats actually have a cost.)
The four encounters per day expected in DnD are too much. Often I feel like cutting back on spells/day and power points because of this. It's very hard coming up with three well defined encounters
in a single day without pulling out the random encounters or forcing the players into
yet another dungeon. (At lower levels you're expected to do less encounters ... look at your mage's spell slots available ... and at higher levels you're expected to do more. I really don't want to do six encounters at 14th-level or so in the space of a single day.)
Equipment as attacks in D20 Modern. (Really, I've yet to see a way to get a balanced grenade in-game. Some are too strong when you first get them, and they're all too weak at higher levels.)
Classes with unplayable or nearly unplayable CoCs. Lack of unarmed combat options.
Overuse of prestige classes, Complete Warrior, power creep, obviously broken or unclear stuff ending up in rulebooks, and a near-universal refusal to work on some high-level fighter feats. Even BoIM didn't cover this
Elven subraces. Half-dragons (draconic template is better), vampires (SKR's fleshbound template is better).
Strength. Really, much better than in 2e, but having a high Strength is overpowered at early levels (a 1st-level fighter with a greatsword doing 2d6+3 damage can kick my 1st-level rogue's 7 hit point behind
and quick).
