There were some, but only a handful. Yeah, MM2 is one of them. Manual of the Planes is another (though the 3.5 players' version of it trod much of the same ground.) Apart from MM2, most of the books that weren't re-released were either niche products (Ghostwalk) or mostly flavor text (Living Greyhawk Gazeteer). The lion's share, including all popular books, were re-released, though, including all player-centric books (either in the Complete series or stuff like the Expanded Psionics Handbook).
One of the main differences I see is that I'd never, ever consider the 3.5 PHB a "supplement" for the 3.0 PHB. They were not designed to be used at the same table with one another, and there's zero value added from doing so. Ditto, two books like Sword and Fist vs. Complete Warrior. On the other hand, Essentials was designed both as a supplement and as a new starting point for beginners; I think adding the HotFx books to my PHB is pretty awesome.
WotC was very, very clear that 3.5 was a new edition. I tend to take the publisher's word for this sort of thing because it's the only metric that really makes sense across the entire RPG hobby. The player base was extremely clear about the divide, too - the edition change was one of the main driving forces behind the collapse of 3e's third party publisher market.
-O