Well, a lot of games are seen as over-rated because people expected too much from them. Personally, I'd put Deus Ex 2 on the list (not top of the list, though) for that exact reason.
The original was brilliant (if sluggish), the new version could never be as good as I wanted it, but they could at least have *tried*... The game is slow as hell (even when compared to the original), has very small levels, and really doesn't allow you a lot of choices of where to go or what to do. On the other hand, if only the graphics engine was faster, the levels larger, the game longer, the replay value greater... it could have been perfect.
Kinda like Vampire The Masquerade: Bloodlines; it's a great game, but it's too short, too small, too buggy at times. I can't wait for a sequel or expansion pack, but I'm afraid that new version will be worse, and it'll become the new "most overrated game of all time"...