This is an interesting thread. I have to admit, I agree with some of the statements made. At times it seems like MP lacks motivation. For me, however, it's not so much the storyline (generally I don't really care about a game's storyline) but the level design. Super Metroid had you *begging* for that Grappling Hook or Speed Boost. I didn't really feel this with MP. Generally, MP gave me items pretty soon after I started needing it. Some items were a complete surprise, and only necessary after I already picked it up, like the x-ray visor or the wave beam. It was a great game, but the items weren't as satisfying as in Super Metroid. I also wish there were more creative items besides beams and morph ball stuff. Maybe some close range weapons (like Samus's flamethrower from SSB/M) would be nice.
As for the scanning... well, I loved it at first, but it got tedious after a while. They all seem to be the same - either some mystical prophecy of the Chozo, or technical data from a Space Pirate experiment. Scanning the creatures is fun, though.
I was thinking, what would be an interesting compromise between the log book storyline and cut scenes / dialog would be audio/video data that you can download. It could have, for example, a surveillance video of a recent attack by Chozo ghosts or something, and then have it black out at the last minute. Or it could have a surreal telepathic vision of a Chozo prophecy. It'd still retain the feeling of being alone on a mission, but I think it'd help strengthen the plot quite a bit.
I would really like a transporter system implemented - I never really loved backtracking across the entire game in Metroid games, especially when you find that that secret you've been dying to uncover is a missile add-on or something.
One other complaint I heard (from the Metroid Database) was the lack of the Screw Attack or a real Space Jump. But personally, I never really liked these in Super Metroid anyway. The unlimited Space Jump was just crazy - suddenly you could fly, and go just about anywhere - it made all the other special jumps obsolete, and it wasn't even that fun to use (constantly tapping the jump button at the right time..). I much prefer the Space Jump in MP, which is very fun to use and has a great feel to it, which is especially surprising in 3D. It would be cool to see the return of the Speed Boost, though..