Mostly I've enjoyed 3.5, but there are legacy issues that I have had trouble with, as well as mechanics that just don't seem to work as intended.
• Vancian spellcasting.
• Monsters that are time-consuming to prepare and hard to utilize. Our DM is smart, but forgets to use monster feats all the time. He's the improvisational type, not the hours of prep type.
• SoD spells and level-drains.
• Why am I playing a rogue when a wizard gets you all that and a bag of chips?
• Prestige Classes; narrowly defined campaign-specific fluff, or rules-breaking munchkinism? You decide!
• Use Rope skill. What's with that? Bondage R Us.
• Challenge Ratings - they never worked right.
• So many skills, so little skill points!
• AC and attack damage only goes up through itemization.
• Too much dependence on a cleric, who gets to run around healing every turn
• Iterative attacks and the AoO penalties discourage movement in combat. Why move when you'd give up 3 swings by doing so?
• Metamagic feats. Great idea, stupid implementation. "I foresee that I will need an increased range on my fireball spell later this afternoon, so I will memorize it that way in place of a more powerful spell". House-ruled right off the bat.
• XP cost for magic-item creation.
• Multi-classing gimps spell-casters.
• High level melee characters are weak compared to high level clerics, wizards, druids and sorcerers.
There are probably other issues, but I'll leave it there. I'm hoping that 4E will fix some of those while still maintaining the flexibility to have characters of the same class not be clones of each other.