A message to Nintendo:

2/2.5d or GTFO

This.

Is this from Nintendo?

I liked the idea of Other M going 2.5-esque wih FP slotted in it, just didn't like the controls they opted for it. If they'd use the nunchuck/wiimote combo for the game, there you could just point at the screen for the first person view and move with the nunchuck. Then you could play throughout the game in both views however you liked.

Not at all, Nintendo will leave Metroid alone, just like they won't produce Zelda, Mario, Pokemon and Donkey Kong games anymore. *sarcasm off*

There has already been a statement from Nintendo along the lines of "you haven't seen the last of Metroid yet" so I'm saying a Wii U release is almost certain. I think a game borrowing from the strengths of Prime and Other M and combining them successfully could be downright brilliant!

This is just off the top of my head: how about a 2.5D game with a similar visual style to Other M, played with the Wii U controller, having a constant first person view on the controller's screen?

It may not be practical for every part of the game, but boy would it be cool!

That would be a good idea, and fix the problem of the duality of Other M's controls

I think they laid a solid base with Other M in terms of making a game with the "feel" of 2D Metroids in a 3D space, and would like to see them continue in that vein, though obviously with a much more tightly-executed story, fewer characters with voices period (Samus and Computer!Adam, who serves a role similar to the Aurora Units of Prime 3 or as he did in Fusion, serving as a guide), and set after Fusion

Maybe focus on Samus rediscovering her Chozo past much like how Other M set up her human past

Yes I'd love a new one. Still go 2.5D or go back to Prime series, no Other M and no story please. Retro should be doing it, but still Retro should be doing many games imo (like DKCR2, why not Strafox? why not something new?), so it's a tough question.

I'd like it to be less linear with a lot more room for exploration and stuff to do besides just progressing the main game. I'd also appreciate more organic alien environments and not just being set on a ship/space station.

Possibly such a game would also benefit from more sophisticated scanning, closer to what we had in the Prime games, perhaps also with visor switching.
I actually don't mind having voiced characters, but they need to be more interesting than the ones we've had so far. How about some Alien NPCs with their own distinct personality and voice handing out occasional tips or information to Samus? That could be cool, in a kind of Private-Investigator sort of way...

My dream feature: Having the option to pilot the ship yourself when moving between planets/locations, in a way that is fun and introduces some new gameplay ideas without breaking what we already have.

I think the first person in-cockpit parts of Prime 3 proved it could work. Imagine exploring the hull of a huge space-cruiser with your ship's flashlights shining on it in the darkness of space to look for clues, etc..
Or imagine navigating an underwater ravine on an alien planet before finding a proper place on the bottom to dock your ship and go out exploring.

I honestly believe the ship could be further used to introduce a new mode of play, in addition to the regular and morph-ball ones.

Besides, Starfox is more arcadey and twitchy than that...

And seeing as Metroid already has FPS elements, third person adventure elements, Morph-ball puzzles, combat, platforming, navigation puzzles,  utility upgrades and scanning, I'd say purity has never been the name of this game.