I only DM D&D. The bad things about DMing 3.x were:
-Spells the break the plot. I never like how teleportation worked. Travelling was always the fun part of my games. Some divinations and resurection spells too
-How CR works. I like big encounters. I never liked running a series of small randomic encounters. It was hard to put many low CR monsters in an encouter because os the encounter would be too easy, with a well placed area spell, or too long and tedious.
-Magic Items. I like magic items be a special thing in the game, but when characters need to have them or the game doesn't work, they become predictable and boring, and the game looks silly.
-Characters that need to stop. It was a pain in the back to arrange the adventure always having to expect when the character were in need resting to regain powers. When the characters enter the dungeon, they should leave it only when they finished it.
-NPC creation. I never ever, in the last 8 years, created NPCs using the rules that were provided. Actually, I always created NPCs using what I think will be the 4E philosophy. Make up what you need when ou need it, using guidelines to make it balanced. The guidelines were always in my head. I prefer to have a DMG that helps me improve my style of Dming than having a DMG that give me rules I'll never use.
-Low level play too dangerous, if I tried to put a little more threat, there was a big chance of TPK. It was like walking on eggs. High level game too slow.
Those are the first that came to my mind, threre are other minor issues of course. 4E seems to be fixing all of these, so I'm thankful.