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http://bulk.destructoid.com/ul/user/4/40209-147330-normandy01456x213jpg-620x.jpg
The Normandy (Mass Effect)

vs.

http://g-ecx.images-amazon.com/images/G/01/ciu/4a/5f/eb9f228348a065e82bc7e010.L.jpg
Samus'es Ship (Metroid Prime 3)


Fight is in space.

Which ship will win?

Um, probably Samus' Gunship, but I am not totally sure.

If relevent, is there a noticeable size difference?

The gunship is more akin to a star fighter than a full fledged ship, seeing as how it's large enough to fit Samus comfortably. The Normandy can house a full crew, which is needed for peak performance. Do we have any combat feats for either vessel?