I probably shouldn't have, but yesterday I bought BOTH! Both are awesome, but neither is getting the time it deserves. Anyhoo, Metroid's t.v. spots are the opposite of what Nintendo should be showing. If they had a campaign like Prime 1 had, I would say Metroid wins easily. So far, the game seems damn near flawless.
Bioshock is also pretty friggin' sweet. I hope everyone picks it up despite it's lack of multi-player. I'm really spreading the word on this gem!
The biggest problem both franchises have is image. Metroid is a fast paced adventure with a cinematic feel, and incredible control, but the first two were so slow and deliberate. Bioshock pretty much perfect, but many think it's just another FPS. Worse yet, most have never heard of it. I figure both games run the risk of being overlooked by the mass market(overshadowed by more hyped games), but if I had to guess, I say Metroid takes it by a small margin.