I don't think Metroid necissarily needs to be REBOOTED....but I do think it would be a healthy choice to just completely ignore the entire Adam Malkovich BS (and also, just the Fusion Suit), from Fusion and Other M.
Let's say I would support a sort of "soft reboot", where we scale it back to Metroid III (Super Metroid) being the last thing that chronologically happened with Samus. Honestly, thus far, while I like the Prime games, Metroid 1-3 are the only games that really deserve "hard cannon" status anyway. The Prime games are just "stuff that happened in between", side story, nothing of extreme consequence really happened, as far as the overall Samus story goes.
I've said so many many times, but what I want, is a direct sequel to Super Metroid that is what Metroid IV (Fusion) SHOULD have been. Fusion was not a BAD game by any means, but Metroid should not be linear like that. And them trying to shove heavy story elements into a franchise that up till then was very LIGHT on story (in game), just wasn't right. What we SHOULD get, and what I want to see, is a 2D (fully 2D, no polygons) Super Metroid successor that actually lives up to the heights of that game. I have long dreamed of a gorgeous looking, hand drawn 2D Metroid, in HD, and if the next console really DOES wind up being some kind of console/portable hybrid, that would be the best time to do that.
That is what I want, for Metroid, more than anything else. I could honestly give a damn whether or not they ever make another Prime game, even though I DID enjoy Prime 1 and especially 3 a lot. I just don't need to see a new one, even if the graphics ARE super pretty. I would far rather see Retro work on something original, their own IP.
As for Zero Mission though, I don't think that game deserves any crap. It was a nice remake, and I really enjoyed it (in fact I'm still waiting for them to release it on VC for Wii U in NA). I'd REALLY like them to give a Zero Mission, 16-bit remake style treatment to Metroid II, as that game is honestly the forgotten child in that series, and would benefit greatly from fans being able to replay it, in full color, with a Super Metroid makeover. THAT would be something I'd be totally excited for also.