Beyond Good and Evil wasn't a perfect game. It was a little too short...
...and that's about it really.
Everything else is just fucking awesome! Who woulda thought that a game with forced vehical, stealth, and "run-away" sections could not just be playable, but also be more fun than a barrel of the most wimsical monkies. The controls are tight and fluid, the story is above average, the characters are interesting and deep (Double H FTW), the environments and overall art deco are gorgeous, the puzzles are clever, and the sence of scope is immense.
Basically, Beyond Good and Evil is what a Zelda game would be if Miyamoto and the rest of Nintendo had balls.