If a Space Pirate game was something that could be told in 2D, I wouldn't have any problem with that.
Being a Pirate unit of some sort, that starts out as a grunt, and then is continually "mutated" into a bad-ass that could possibly rival Samus (but never fights her in-game)? That would be an interesting plot arc. And if nothing else, they can still utilize Metroid-style mechanics, just in a different context.
...Just....give me a break from the Prime-style games. At least Zelda has been giving me "classic style" games on the GBA and DS, all while Link continues his thing in 3D on the GC and Wii. I need something similar from Metroid on the DS, as well!