Despite the major plot in Fusion, I would think that if they had to base it on any particular game, the original (or rather, Zero Mission), Prime, or Super would work best. I don't think they'd draw much from Return of Samus. They mentioned the Space Pirates and Mother Brain...whether they come to be in a possible Metroid film (which may or may not come to be itself) remains to be seen. But that must mean that they at least like Super and/or Zero Mission.
The first choice in my mind for Samus (note that I said first, not best, feel free to come up with better ideas) is Bridgette Wilson. With only Samus in most of the games, there really aren't many others to cast...unless you think Ridley should be coherent (as he was in the Nintendo Power comic and Japanese web e-manga) and they'd likely cast some other bounty hunters, space travelers, or scientists.