I'm a little late on this thread, but a lot of my problems with MP have already been mentioned.
Pretty disappointing for me because I pretty much bought a Gamecube (although only for 99 dollars) just so I could play this game. Especially considering all the hype it got (some people putting it in their top 10 of all time).
The scanning was just ridiculous and clumsy how they handled it. It almost seemed like an artificial way to increase the playtime of the overall game. It was initially interesting because I wanted to scan everything in the space ship to figure out what happened .. but once you make it to the planet, I could give a fuck less.
The boss battles were equally unimpressive. Figure out the pattern/trick, die, try again and win. Although to be fair, I only fought the first three before I quit the game.
The slow movement is what really killed it for me. It wasn't noticeable on the first section because the ship has a lot of small rooms and corridors. But once you get to the planet and have huge expanses of nothingness you have to cross, it takes FOREVER. Especially if you know you have to backtrack to a certain location .. it just eats your soul.
I have picked up the game three times in attempts to play through it (just because so many people have raved about it). It's just a bad game, period. It's not because it is Metroid either .. it could have been called Amazon Warrior Princess on Planet X .. and it still would have sucked.