1. The books are not well organized. None of the D&D books have been great when it comes to organization, but I was downright confused by the organization and information set-up of the new books. It took nearly a full read-through for me to find some of the information that I was looking for, and I'm still perplexed as to why they placed some of their information where they did.
2. The game under-powers characters. To a degree, I like this point as I feel that 3.5 (and 3.6) make characters a little too over-powered, but (as my wife pointed out to me) the point of playing these games is to be a person who's larger than life. Capping ability scores at 20 and magic bonuses at +3 are artificial ways to "balance" the game (and will no doubt be amended with later books).
3. The books are expensive. Third edition came out at $20 a book. 3.5 books were around $30 a book. Granted, that was 14 years ago, but these new books are $50 a book. I already have hundreds of dollars worth of 3.5 books (many given to me as gifts from friends, some bought at discount), and my friends have put a good deal of money into that system as well. Having everyone (or at least every family) who plays with us put up at least $50 for the Player's Handbook seems a bit steep.
That said, I do like some of the changes (especially the additions of advantage, disadvantage, inspiration, and hero points) and have incorporated them into my own Home-brewed D&D 3.6, as well as some other changes.