There is nothing wrong with the rules of 3.x per se. In fact, the third edition rules (3.0 moreso than 3.5) are by far the best rules set that the D&D game has ever had.
What's wrong with 3.x is not the rules, but the presentation. It's not the rules that suck, its the maturity of the advice that goes along with them. If you read the 1st edition DMG, rulewise its an absolute mess, and some of the advice EGG gives is very suspect. (In fact, he specifically mentions that thier were failures to communicate in earlier books that created problems, for example people taking too literally the random treasure charts, so its not like he's unaware of problems.) But he never treats the DM as stupid, and he's clearly writing to the DM in a 'peer to peer' tone. If you read the 3.x edition DMG, you get the impression that the writer thinks the reader is too stupid to conduct a game with the grace and elegance that the author himself most certainly does, and so instead of writing 'peer to peer', he lays down some really juvenile guidelines for how to run a campaign designed to get say a 12 year old kid up and running as a reasonable DM on his way to maturity. I suppose they working with the assumption that most DM's are head strong creative people and will eventually grow out of any stricture you lay upon them, develop house rules, homebrews, and different styles of play. But the problem with this is that 3.x is also a much more player oriented game in presentation than earlier editions (I'm fairly certain the justification for this is economic and not game value), and as a result it tends to foster DM/Player conflict. There is an increasing assumption amongst players that 'grew up' on 3rd edition that if the DM's style doesn't exactly match that of the DMG, that he's somehow 'breaking the rules'.
Witness the many posts of the sort, "If the DM gives me what my character needs, rather than what I the player want my character to have, then he's a power-tripping ego maniacal RBDM and I don't want to play with a jerk like that." It strikes me as infantile whining, but its repeatedly what I've encountered from newer players on the board and IRL.
So, for my part, I'm a huge fan of 3rd edition. I think its great. I think its alot better of an edition than any previous edition rules wise, and its basically the rules set I was trying to create with all my tweaks of earlier editions. On the other hand, I loved playing BD&D and 1st edition, and I'm not interested in an edition wars thread. To the extent that I can sympathize with the grognards that think earlier editions were a better game, I think 3rd editions sucks worse than any other edition as a guideline to running an interesting campaign, or being creative, or being a good roleplayer. I don't know if it is the CRPG influence that earlier editions didn't have to cope with, or what (because no CRPG I know gives players what they want rather than what they need unless they enter cheat codes), but the number of "Cry me a river! My DM didn't let me buy a +5 holy sword in the nearest town!" posts that EnWorld gets month after month, leads me to think that there is something very limited in the way people are encouraged to think about the game.