This thread should not be labeled MC vs Samus, it should be labelled Spartan II vs Samus or Halo vs Metroid. You can't compare these two individuals because we have never seen them fight in similar circumstances. The chief would lose a fight to Samus because he is many years behind her in his technology. Each of these hero's does very well in their own world because each of them is built for their world.
To use the games as a reference is unfair, but it's all we have. Again, they are both excellent soldiers, but Samus has the advantage of her technology.
Well, MC would have a very hard time in Samus's world, in Samus's present time frame, but if MC was in her world at time similar to the Halo universe then it would make thing's more fair. I'll put it this way, I think MC is a better soldier, but Samus would most likely win a fight because she has much better technology. If you gave the MC some type of weapon on par with Samus's in her world, he'd be able to do her job, but the problem is, the MC has a Battle Rifle, Samus's weapons would make a Battle Rifle melt just by looking at them.
And yes, a single flood falls easier than a metroid, on normal, or easy, but there are alot more flood than metroids.
Yes, Elites in Halo One tend to stand still for a few seconds while they shoot, on easy, or normal, trying playing on legendary, or legendary on Halo 2, or even heroic, they use their cover, and they only tend to stand still usually when the player is cowering behind something. ((Yes I've done that))
And MC has faster reflexes, his suit is designed to react as fast as his thoughts, and with the genetic experiments done on his cortext, he has very fast thoughts.
As for speed, the MC can run about 40mph
As for intellegence, I think that's very close, but MC was trained with the most extreme of ODST drills when he was only 7 years old. He is very cunning.
The problem with the Battle Rifle is that it's probably underpowered against Samus, give him a MAC Combat Assault Rifle prototype and then that help. As for the sword, I don't think Samus would ever let him get close enough to use a sword.
I think the Master Chief is a better soldier, but I think Samus would win in a fight.