My dream would be a 3ds 2d metroid game by Retro which story leads into Metrio Prime 4 on Wiiu.  I don't want a 3d prime on 3ds unless it supports the circle pad expansion and even then I'd prefer a 2d one on 3ds. With the budget the game would have on 3ds they'd get a better game out into the wild by going 2d.

Fake!

Definitely wouldn't work as well as with Smash Bros for several reasons

1: Smash Bros is less graphically intensive. Brawl (sans textures and resolution issues, i'm talking more strictly in poly-count) was clearly "good enough." Metroid Prime was a lavishly rendered game, the kind of thing where the Wii U/3DS difference would be easily, instantaneously noticeable in Wii U's favor.
2. It's easier to differentiate the Smash Bros experience. You can put the same basic game down on two platforms, and then change up some characters or some game modes and create an experience that is different enough, and do so easily. A Metroid game of any sort (let alone a 3D one likely to be assest-heavy) would be hard to differentiate.

3DS 2D Metroid with two screens... me gusta

Will be the first Metroidvania (-vania because please no levels on my metroid) featuring a map. That's touching

Think about my post for a bit, look at the one above it, then i'm sure you'll understand.

A "Super Metroid" type game on 3DS?  Make this happen! 

Utterly terrible idea.

The sole thought of pleasing home console-, as well as handheld users at the same time is rotten to the core.

If true, I wonder if you get both for the same price, like how Sony is doing it

Bad idea, I'm only buying one of version of each.

Seems like a poor idea, but a release of 2 games with cross-function would be cool.