I had issues with 3.5- mostly related to imbalance issues (when I DMed it was almost entirely low-magic campaigns) and overcomplications.

4e fixed everything I hated about it. Unfortunately, it had it's own issues, mostly related to overly long battles and choice paralysis, which I won't bore you with.

Nowadays, if I run d20, I run pathfinder (homebrewed for low magic settings) or Saga- in my mind, the best d20 system would incorporate the class/level/abilities and feat choice system of saga and the action economy/defences/BAB/simplified attack and skill system of 4e. But I doubt I'll see that any time soon.

Right now I'm running Savage Worlds. I'll think I'll stick with this for a while.