3.5 improved the rules which seem to go smoother in more cases and have less problems.
However, it had a bad effect on our games. Most of the players bought 3.0 books and didn't want to spend more money on 3.5 books, but are still using the old books to look up for rules. This makes a lot of confusion and lead players to make tactical mistakes.
The best thing to do is either stick to 3.0 or move to 3.5 completely, but that wasn't eventually possible in our case. We are actually playing different campaigns with the two ruleset, to please everyone.
Another bad effect was to partially invalidate some published material. I would have preferred 3.5 to invalidate everything, but this is just my own preference, that I hate having a book which is only partially valid such as FRCS or DotF, and I have to buy a new equivalent book (PGtF or CD) which updates only part of the old book... then I am left with the doubt of what I have to do with the material that was not updated, and with 2 books to use in place of one.*
Since the 3.5 material is anyway better on the overall, if there is something to blame WotC about 3.5 is that it should have been the first version of 3rd edition since the start, or at least it should have come out much earlier, before releasing so many accessory books. Some of the 3.5 bits were so clearly troublesome that it is hard to believe that good playtesting would have missed them.
* (edit) I think this is especially bad for FR players.
If you play 3.0, more or less you have to live with the books published before the revision, otherwise you will buy books with are not fully compatible, and you'll have to "retro-adapt" with 3.0.
If you play 3.5, you STILL have to buy a FRCS, a Magic of Faerun, a Monster of Faerun, and/or old regional books, for some important information, only that you already know that only part of those book will be usable - except that you have to pay all of it.
From a customer perspective, it's a very bad result.