Unlike the Zelda series poll on this forum, this question is a no-brainer. SUPER METROID!
Metroid set a good foundation. Metroid II established the trend of new upgrades and challenges. These two built into Super Metroid, which took everything that worked from 1 and 2, and added even more. No Metroidvania has come close, even Symphony of the Night. The only Metroid to come close, 2D or 3D, is the first Prime entry. For me Super Metroid is easily among the best games ever made.
The other 2D entries: Fusion had a good story setup, but was far too linear and didn't really add much. Zero Mission was like a light remake of Super Metroid using the shell of the original Metroid. It was a lot of fun--more so than Fusion-- but too easy and it ultimately felt too much like a retread (though, it was an enhanced remake of the original NES Metroid game, so that's to be expected). The new comic book-esque art-style was attractive, but it also lightened the overall atmosphere a bit. I liked the ledge grab ability added to Fusion and Zero Mission, but the pace of Zero Mission's character was way too fast. The Zero Suit segment was OK, but not necessary in the larger scheme of things and leans more toward fan-service.
I had hoped 'Metroid Dread' would be made, but who knows. I'd like a new 2D one for DS that really pushes the formula beyond Super Metroid and continues the story after Fusion. And, PLEASE, no lazy top screen = map screen junk. That's such a waste.
But, in some ways, I'd like an epic 3RD PERSON Metroid game even more. I still have hard feelings over the limitations of having 3D Metroid be first-person (outside of the Morph Ball).
Regarding the Metroidvanias...I think they've been lazy and lackluster for quite some time. Metroid could still show'em a thing or two. But who knows if it'll happen since Nintendo has decided in recent years that Samus is their [unneeded] answer to Halo.