I'm a huge metroid fan. Metroid is my favorite game franchise of all time. I've put some thought into this, and here is what I think the 3DS version should have:
1. Metroid 5, it should be a sequel to fusion. The ending of Fusion left some interesting plot threads that still haven't been touched on. I think that they should expand on this.
2. No voice acting for Samus. I'm fine for Samus talking, as long as it is in text form. Fusion actually did a good job of this. Also, Sakamoto better not be writing any of the dialogue or story.
3. Focus on exploration. Metroid Prime 3, Other M, and fusion really strayed away from the exploration aspects that make the Metroid series so amazing. No more of that, I want it to be like Super Metroid/Prime.
4. Make it 2D, the 3DS could do a prime game, if it controlled like Prime 1 on the gamecube, but frankly, a 2D game would look better on the limited hardware, and I think that 2D Metroid is made for handhelds. Since we won't be getting a 2D Metroid on consoles, best to leave that part of the series on handhelds. There is still a large audience for a 2D Metroid.
5. New Powerups and bosses. Metroid Other M had nothing new. They rehashed bosses, powerups, and the aesthetic was same old same old as well. The Prime games really blazed new trails for the Metroid franchise, if I want to fight the old bosses, or use the old powerups, I'll go back and play the old games.
6.Keep the story light. Don't do an Other M ever again. Even if the story in Other M was great (It was terrible) it would still be taking away from the focus of Metroid: Gameplay.
7. Isolation is key. Metriod Prime 3, and Other M featured a lot of side characters. That's not what I want in Metroid dammit. I want a huge alien world, where I am alone. The feeling of Isolation is one way that Metroid is awesome. Don't take that away. Atmosphere is so key, and when I'm alone on an alien planet, with creep/awesome music, I am happy.
8. Don't let Sakamoto any where near it, he's a joke, and doesn't know how to make a good metroid game.
Can't wait for this, I buy Nintendo systems for Metroid. Fingers crossed for a reveal at E3!