Since the first Metroid Prime came out, Retro's released one game on average every 2-3 years. Since they're last game came out in August 2007, the earliest we'd see a new game from them would be end of summer 2009.
Since Nintendo doesn't announce games now until a few months before release, if Retro has something coming out at the end of summer or even the fall, E3 20009 will probably be the first time we'll hear about it.