I wouldn't go so far as to say the Prime series sucks (as I have barely played any of them), but I do agree we need a 2D Metroid game. Maybe even a game that takes place AFTER Fusion! GASP, unheard of! They could bring back the enabling and disabling of items, as I've never really gotten to experience that. They could have grapling beam upgrades, and a play area bigger than Super's. I don't see how it would have to be a story with Samus clearing her name, since I don't think the Federation (I always think that sounds was too much like Star Trek >.>) would lock Samus up in jail or anything. And, if it doesn't take place in a Federation facility, then they could skip over the order giving. If it takes place on an unfriendly planet.... Yeah.
DS Features Time
The action could take place on the lower screen, with the status menu on the top screen. When you press start, the screens switch around, the gameplay pauses, and you can access the pause menu. You of course have the status screen, the map screen, and the super duper power saving Sleep Mode! When actually playing the game:
Items
To activate the speed booster, you not only have to have neough space, you have to slide the stylus in the direction you're running. To use the grapple beam, tap the grapple point you want to grapple to. To fill your tanks with reserve energy, you drag energy from the on-screen reserve tank display to the health display.
That's all I've got for now... I kind of went overboard. >.>