There is currently no mainline Metriod Prime game in development according to Prime's producer(and a bit of info on where the series will go in the future)

[Darwinianevolution]

If Metroid games really take that much time, why aren't they working on it right now? Starfox Zero was going to be a Wii game, Pikmin 3 was a Wii game, Kirby Return to Dreamland was a GC title... If you fear you won't have it for the current console, start now and just move it if needed.