I have to agree that Beyond Good and Evil is overrated. It's still a very good game, and I'd recommend it to most people (stealth haters aside), but for me it's not in the same league as Zelda or Okami. The hoverboat/craft thing you fly around the overworld is good fun though. The story is well told too, I just don't think the core gameplay is particularly great. Plus I found the length of the game and size of the world to be slightly underwhelming. I wish Michel Ancel would make a new Rayman platformer, BG&E has a few parts that are reminiscent (mostly in the environments) of Rayman 2.
Anyway, my vote goes to Perfect Dark. I got stuck on a mission several months ago and I need an excuse to get back to it, because up until that point I'd found the missions pretty decent. And considering I've unlocked the 007 difficulty mode on Goldeneye it's frankly pitiful that I haven't even finished Perfect Dark on the easiest difficulty.