Because I have played only a little 3E, I'm curious as to the problems devoted players have found with it. I'm sure they're not the fundamental ones that ensured I would not DM it!
Apparently, there are some issues with high-level play. Are they in the core rules, or a product of piling on supplements?
Both. The ELH is poorly written (to put it nicely). To be fair, though, an early copy of the playtest rules got leaked, which I think forced them to go to print way earlier than they'd planned - the final copy is riddled with mistakes that even a novice game designer wouldn't have made.
However, the epic system is, on the whole, really badly designed. The system itself is more of an add-on than logical extension; at L20, you're suddenly "EPIC", like you wake up one morning and you've become "more human than human". You gain access to "epic feats", your BAB and saves change to follow a fixed progression, and you don't gain any more new class abilities. The numbers keep increasing into infinity because they made no attempt to figure out how to account for increasing power levels; monsters have hundreds of HD, immunity to everything, and SR so high it's nearly impossible to affect them with a spell, which means you have to a) attack their weak save(s), or b) engage in an endless hackfest to whittle down their hit points.
The epic spellcasting system is a steaming pile of crap. It uses Spellcraft to rate spells instead of going by level, which means that it requires skill mastery (the concept, not the feat); players quickly figured out they could create spells to boost their Int by ridiculous amounts, which gave them a huge bonus to Spellcraft, which let them cast other, more powerful spells... And then they are ritual spells. Since each additional caster reduces the Spellcraft DC, you can simply round up a few dozen (or hundred) other spellcasters to cast a massive ritual with a DC of 10, 5, or even 0.
On the other side of the fence, the sheer amount of supplements obviously creates problems - you can't possibly account for all the combos of classes, templates, and PrCs which, though they might be compatible and perfectly balanced with the core rules on their own, could become broken to various degrees when used in the proper combination. Add to that that the CR system falls apart at the higher levels, which makes it very hard for a DM to choose an accurate threat for his high-level party, and you can see why a lot of people gripe about it.
This is a large part of why 4E is capped at 30th level - the designers KNOW that high-level play is broken, and they either didn't know how to fix it, or didn't want to expend the effort to figure out how (or both). Instead, they said "Let's see... a lot of people like playing epic, so let's put a hard cap on play - L30. This gives them a chance to play semi-godlike PCs, but we can control how the system works and ensure that things remain more balanced. Everyone wins!" In that regard, they succeeded - high-level play is indeed balanced, from what I've heard and seen (I don't actually play 4E myself), though the combats are still a grindfest.
A workable high-level system is something I wanted to see done (and done well) in 4E, but having to play a completely different game to get it isn't worth it for me. Unfortunately, as someone mentioned, I don't think a re-revision of the 3E rules would have flown with the majority of gamers. If they'd held off on 3.5 for a few more years, included more (and better) changes, and repackaged it as 4E, then probably - it would've been comparable to the change between 1E and 2E. I won't say 3.5 wasn't necessary, because it was, but I think they jumped the gun putting out what amounted to errata and bugfixes instead of releasing a fully revised system that incorporated the best of the existing material.