According to a recent interview with development heads Shigeru Miyamoto and Shinya Takahashi, both 2D and 3D Metroid titles are currently in the works (although in the early planning stages).
When prompted, Takahashi stated the following:
So it has been a while since we released the last one and we’re having discussions internally about what we can do next. So at this point we have two different types of Metroid games. We have the Prime style of Metroid game and we have the more traditional style of Metroid game. We feel that we do need to take care of both of these styles of play. And the hope is that at some point in the near future we’ll be able to share something about them.
This is excellent news for many Nintendo fans who have been awaiting a Metroid title since the Prime series for Gamecube and Other M for Wii.