Not to get off topic (though that's the name of the game now!), but I really liked the first Metroid Prime. I think the UI elements were amazing, as was how much detail the worlds had. But, they should (funnily enough) take a cue from some of the Alien games and go for some quick thrills and bursts of enemy encounters, more than what they already did. Keep it real moody.
Oh, and with all the scanning. It's awesome to get the story revealed the way they did it, but the scanning got a bit out of hand. They should have Samus, say, enter a ship, get a dying computer with an unfinished message on it trying to get sent out, and then you're left to your devices to go around and figure it out, complete the level, find the weapon, etc.
They just need to tighten and somewhat modernize the style is all. Metroid Prime had so much going for it.
That said, seeing a new 2D Metroid would be great as well, but there's no reason why they couldn't have both.