Prime with new areas.
Seriously, I don't think Super Metroid is the holy grail of all that is action-adventure. But I DO think the guys currently in charge of the franchise could learn a lot from playing some of the older games.
Or possibly just thinking about the design decisions they're emulating.
You will never convince me that timed escape sequence + super-powerful final boss is anything other than a BAD IDEA.
They're caught between "Metroid has timed escape sequences, we have to have a timed escape sequence!" and "ALL games end with a final boss battle! It HAS to be the last thing the player does!" and they don't even realize it's a bad idea.
Zero Mission is, as I said, a great improvement over the team's first attempt. It's possible that in another game or two, the current producer may start making good Metroid games. But I'm not sure of that.
What do I want to see for the next Metroid...
Remove current producer Takehiro Izushi from the 2D side of the franchise.
Remove current producer Kensuke Tanabe from the 3D side.
Another Prime should have Kenji Miki as sole producer. He has an established track record as coproducer on Prime 1 and Prime 2. With Miyamoto having stated he exerted very little influence on Prime 1, that leaves Miki as the man in charge.
He isn't on Prime 3, and the bad parts of Prime 2 seem to have become the entire game in his absence, while Mr. Tanabe has moved from coproducer of 2 to sole producer of 3.
The math seems pretty clear to me.
As far as 2D games go, Mr. Miki may make a good producer there, too.
Makoto Kanoh would certainly be another option, if he still works for Nintendo. He's been with the franchise since day one, and certainly proved himself capable of producing a good 2D game with Super Metroid.
Not quite what you were expecting, is it?
In terms of gameplay, there's one long-standing dream I've wanted to see...
Take the SNES MechWarrior's "everyday life" and equipment upgrade segments, Super Metroid's Metroidness(or Prime 1's, depending on how you want to go), and the Super Star Wars trilogy's mixed-mode gameplay, throw them all in a blender, and create a more general Samus Aran game.
A game where Samus can gather information, pick her missions, fly around the galaxy to different planets at will, engage in epic space dogfights, run through caves in the platformer adventure segments we all know and love, get paid, spend cash on ship and suit upgrades(not abandoning the traditional pickup mechanism, just augmenting it), etc.
A game even MORE free-form than the original Metroid, with enough depth and variety to keep it fresh for years to come.
There's so much you can do beyond "ZOMG PIRATES! AND METROIDS! KILL!" that's never been explored.
And as time goes on, a game of such epic proportions becomes ever less likely. Games become more expensive every generation, and the risks such a title entails become less appealing. ESPECIALLY with a valuable property like Metroid.
*sigh*