Metroid was a 2D game, yet the 3D games on the Cube, were some of the best in the franchise. A 3D Mega Man can work, if you stick to the aesthetic and established rules.
I like Metroid Prime, I just don't think it would work as well for MM, at least IMO. They both started off as 2D shooters, but have pretty different atmosphere's. MM is a bit faster paced, has a more cartoony vibe, and has more of a fun feel to it. Metroid is slowed down a little, and has a slight dark, melancholy feeling.
I think Metroid's setting works better in an FPS. I could easily see Metroid's world in a more real world sci-fi setting. Metroid also lends itself to first person exploration better.
MM has a bit too much energy to it for that to work, IMO. Doing things like wall jumps, sliding, charging, flying, building your own platforms with ice, and so on, and so on, don't lend themselves well to a first person perspective. Neither do the enemies, with the way the bosses function in particular. A 3rd person perspective allows for better movement, and can allow for things like bosses tunneling behind you, or bouncing attacks off of surfaces better.
First person shooters tend to feel, for a lack of a better term atm, too western. They're typically gritty, violent, and follow more real world physics. I just don't think I'd enjoy a MM game set in that setting nearly as well as a 3rd person. Though I'm sure it'd sell, and probably wouldn't even be a horrible game. I'm just speaking to personal preference, and feelings on it. I don't think a game like that would be for me.