* Facing (now called space) is now always square. In order to facilitate miniatures play (apparently), horses are no longer 5 feet by 10 feet when you put them on a grid, they're a 10-foot square. The horse has to "squeeze" to get through a 5 foot wide space. Three 9-foot-tall ogres require a 30-foot-wide passage in order to walk abreast. D&D, with its already abstract combat system, did not need this extra layer of abstraction. Not to mention the fact that this changes game play in strange ways, such as how many of the charging ogres you can get with your fireball spell.
* The game has an even stronger focus on miniatures. 3.0 had a strong focus on miniatures, but we wanted to at least address the fact that you might not want to play the game that way. But everyone in the Wizards of the Coast offices does, and so now you have to as well. And Wizards has a new line of miniatures to sell you. Seriously, though, for those wanting to play the game sitting on the couch, the game now offers a new barrier for you. The Combat chapter in the Player's Handbook now reads like a miniatures game. More and more of the game stats use "squares" rather than feet (or both). This is a huge step backward toward the "inches" used in 1st Edition.
* Now weapons are organized by handedness rather than by size. Perhaps the worst change and almost certainly the largest step backward 3.5 has to offer, the new way of handling weapons causes a lot of problems. As you know, in 3.0, weapons were categorized by size, and that size was compared to your own size. So a weapon of your size was a one-handed weapon for you, a weapon one size larger was a two-handed weapon, and a weapon one size smaller was a light weapon. Now, weapons are categorized by handedness, and they do different damage based on size. Thus, it's no longer the case that a longsword is effectively a greatsword for a Small character and a short sword for a Large character. Now, there is a small longsword, a medium longsword (and by implication) a large longsword. So what's the difference between a large longsword and a medium greatsword? About 20 gp. Aside from that bit of humor, though, there's actually a serious design problem here. Because in 3.0, a halfling picks up a magical longsword and uses it in two hands -- no problem. In 3.5, that longsword (presumably a medium longsword) is -2 in the halfling's hands because it's the "wrong size." The DMG doesn't hint one way or the other, but logic assumes that you've either got to roll randomly to determine the size of the magic sword in the treasure hoard, decreasing the chances that any given character will actually find treasure he can use -- and that's not fun. It's more complicated, it's clunky, and it hurts game play.
* The NPC tables in the DMG are now more open ended, and thus less useful. The NPC tables used to be there when you needed a 7th-level fighter or a 13th-level rogue right then and there, in the middle of a game. They came completely statted up and equipped. Now, if you want to use them in that way, you've got to stop in the middle of the game and decide which weapons the fighter uses and spend 8,000 gp on gear for the rogue. Thus, they are useless for the original goal. I guess the designers felt the charts were "boring," because you got the same 7th-level fighter every time. Now, they are clearly meant to be used as pre-game development aids to help make NPCs. Unfortunately, each 7th-level fighter is still going to be an awful lot like every other one using this method. What's more, if you're not in the middle of the game, there's no reason not to just make one up from scratch (or use one of the excellent character generators out there, many of which are free online).