Issue # 1 for me:
Magic item creep is the biggest problem I have with 3.X games. I have replaced all creation feats with equivalents that allow temporary versions of rings, wands, etc. They last a few weeks, have a finite amount of spells or charges. Players have the items they need, and create them quickly, and as a plus for them, I have removed XP cost for creating items. So far, my players seem to like the change.
Issue # 2 for me:
High level spells can ruin a badly designed game, and it's much easier to nerf the spells than to change your game or module. I have tweaked a few spells so they fit my style, but I also want to encourage my players and not ruin their creativity or fun so will never simply ban a spell. They know (well in advance) what works and how it works...that way they can begin making plans.
There's nothing wrong with high powered gamestyles, but, like anything else they get boring after awhile. If your aim is to defeat enemies, sure, a rod of blasting to that end works great. But, after the 20th time you've used the same tactic it starts to get get boring...and this, I believe is the problem with ultra high magic games. It becomes too convenient not to solve your dilemas, and you can't rationalize it as a character,"Well, I know this works but won't use it because...well, just because I won't."
The trick, is not to give a player too muich power so the adventure gets boring, but not enough to make them feel overwhelmed and helpless. One of the great things about this game is the feel of a challenge, and overcoming it with your wits, or your strength...not just the rod of blasting. This is what is appealing for many of us. Give us too much magic, too many high level spells, or too much magic items, and you feel like it's the equipment/spells that is wining not you.