Both, that have stories that connect. Didn't Fusion's story connect with the Prime Trilogy? I can't remember.

And since it is on one device instead of two, they could even sell it as a physical/digital bundle with both games for cheaper than both individually to increase those sales.

3d of course!

3D now, 2D after that.

2D of course. They could ve at least released a 2d Metroid. Much cheaper to produce than 3D.

2D because Super Metroid is still one of the best games I've ever played.

Also, 2D means it doesn't need to sell like crazy for Nintendo to rationalize keeping the series going.

Honestly, that would only lead to stagnation in its popularity or worse, if they do a 2D games. The Metroid series has so much potential to become one of their biggest franchises!