--Wizards having nothing to do when they've cast all their spells appropriate to the situation
--People having trouble remembering 1-2-1 (YMMV)
--Statting up NPCs, including skill points too fiddly for DMs statting up monsters/NPS (but not PCs--most players seem to like the customization)
--Grappling
--Turning
--Calculating XP from CR
--AoOs too confusing/too many instances to remember
--Too many iterative attacks, contributing (along with SR, miss chance, crit confirmation, etc.) to too much die-rolling
--Players' turns taking too long to resolve due to multiple die-rolls often being required
--CoDzilla (though only if deliberately and expertly exploited)
--Infinite summoning (A summons B summons C summons...)
--Fighters not keeping up as the party level increases
--Scry-Buff-Teleport-Fly combo repeated ad nauseum, and campaign-breaking spells/magic in general (for some this includes resurrection et al)
--Identify
--XP for crafting
--buffing etc., especially remembering which buffs/effects/modifiers are affecting whom and for how long
--useless skills (use rope, craft [baskets], etc. YMMV)
--familiars and animal companions often crappy but time-consuming if used in combat
--save or die
--suckitude of multi-class spellcasters
--HP can vary too much due to fact that they are rolled (YMMV)
--Spell prep takes too long; spell-list resource management too cumbersome
--Necessity and ubiquity of munchkin magic items (Belt of Strength +3 etc.); inclusion of lots of magic items in the CR math
--DR as a primary focus of most combats past a certain level (golf-bag syndrome)