Who do you think would win:
1. Master Chief or Isaac (Dead Space)
Master Chief, easily. Isaac, while quite intelligent, is not a genetically modified Super-Soldier that can lift several tons with ease, has reflexes many times faster than normal humans, has bone density and muscles many times greater than a humans, and has the combat training that Spartans have. It's actually a very one-sided match-up, here. Isaac could have a psychotic episode on John, though. That wouldn't do anything for Isaac but that's at least something...I guess.
2. Darth Vader or Dark Samus (Metroid Prime Series)
I don't see how a moderately Super Human being like Vader can stand up to an energy based life form like Dark Samus. Even if Darth Vader chopped up Dark Samus into pieces, she still would not be dead or even close to defeated. Unless Vader finds some Phazon, he has no way of disrupting her or defeating her.
A better match-up would be Vader vs. Master Chief.