Nintendo wants Federation Force to appeal to Japan.
Metroid Prime: Federation Force, whether you think the game looks alright or not, is not what everyone had in mind when it came to a new installment to the long dormant franchise. The common criticism even to people willing to give the game a chance is that it 'doesn't look like Metroid' with its chibi styled art direction, multiplayer focused gameplay and mechanics, and of course the lack of Samus Aran as a playable character. Everyone is scratching their heads wondering what the hell is Nintendo thinking with this one? I think it's that they're trying to make Metroid look appealing to the Japanese. Metroid, for all of its accolades, hasn't been a hit in Japan, especially compared to other Nintendo properties like Mario, Kirby, and Pokemon. It does okay, but its not the juggernaut of those other IPs, so maybe this is Nintendo's attempt at revitalizing the franchise by appealing to what the Japanese like -- portable game, multiplayer focused, cute -- and work from there. And maybe if the game does alright, then we can get a proper Metroid.
Nintendo knows the Metroidvania genre is overpopulated.
Proper 2D Metroid is nowhere to be seen but its influence is everywhere in the indie scene. Metroidvania games are abundant and are all over STEAM, PSN, and even the Nintendo eShop. And Nintendo knows this, so 'making another 2D Metroid' is not going to be as deal a big as people want it to be, not unless they do something that'll help the game stand out. As for another game in the vein of the 'Prime' trilogy if not a sequel? I don't know, maybe Nintendo are waiting for the NX and are going to drop a bombshell this E3. The only reason I can think of their not being a new first person Metroid is that Retro Studios is either A.) working on it or B.) aren't, and are just doing something else (I prefer the latter because another Metroid game from Retro after all this time would be a bit anti-climatic.)