Hmm...
With Fusion... first time through, it had some very nice twists, and was able to keep an forboding atmosphere of exploration and mystery despite the fact that the whole game takes place on a space station (I was dubious about this at first.)
I hated the way that the computer would lead me around, but by the end of the game I accepted it as a neccesary part of the game as a whole.
Samus controlled really well, but the powerups weren't really anything to speak of.
I loved their evil, evil secrets. I can't get enough of those.
SAX was also an interesting element, but it seemed like you had to know the area aforehend to really get away from it alive. (Zero Mission did a better job at the feel.)
Now, Zero Mission...
Despite it being a remake of the original Metroid, it employed many excellent twists... (ooh hoo hoo... I won't get into that, lest I spoil its excellence.)
It seemed much shorter than Fusion, but upheld the Metroid atmosphere very well.
And even then, it's short length doesn't exactly work against it... This game was so intricately designed so that, if you really knew the area, you could breeze through it, skip parts entirely, and essentially break game.
Except that it was MADE for it!
Once again, they had some fiendish secrets.
Oh, and arguably the best Samus control in a Metroid game.
I'd say Zero Mission was the better game.
Go Moon!