What about Warcraft III? I thought that game was a lot of fun, and definitely better than WC2. I went back and tried to play WC2, but without some of the innovations in RTS in the last 10-15 years (whenever it was I tried to play it again), I found it almost unplayable. For example: you couldn't assign units to a "squad" (1-0) and then send them places...you had to select all units every time you wanted to give an order.
What about Metroid Fusion? Zero Mission was kind of a remake of the original, but it did expand upon it. Either one of those was a pretty solid entry in the series, IMO.