A poll currently running at Nintendo.com asks players about the upcoming sequel to Metroid Prime - whether they would they like to see it returning to a side-scrolling view, as a multiplayer title, with more GBA/GC connectivity, or merely a longer and tougher game. Considering Nintendo's love for industry 180s (the original Metroid Prime and Zelda: Wind Waker are excellent examples of this), it's not likely that the sequel will actually be an FPS title again.
I love how you jump on top of it the moment the idea of it not being what you expected surfaces. They did that with Prime and Wind Waker. I said, no, it'll be okay. I was right. I'm going to be crazy and say it again: it'll be okay!
True - but I'm not sure that means Nintendo will actually do exactly what people want. Personally I want to see a well-executed 3rd person shooter for Metroid with revolutionary camera (or at least as good as the morph ball one) and some well-developed high speed gameplay like the running/jumping skit in Super Metroid. If they can translate that and add to the experience at the same time, I'm all for it.
The problem is that it'd end up being a mature version of Zelda. So they probably won't do that.