There are a lot of things to consider. Especially location and layout of weapons. Bear in mind I honestly don't know enough about Samus or Iron man to make a definite conclusion. If I am wrong on something, please point it out.
For the "Master Chief needs..." argument, we must also take into account that Samus doesn't start will all of her cool power ups either. If we decide that she gets her entire layout, that I believe it follows that MC gets whatever weapon(s) he wants, although a tank would be too much.
Iron Man seems a bit weak (defensive-wise) to me. Personally, I'm throwing out the whole 'survived a tank round' thing because I think that's just ridiculous. The suit might survive but the soft and fleshy Tony Stark would probably be pudding on the inside (possibly some kind of nightmarish Cadbury Cream Egg). Couple that with the fact that he's a normal human (except for the chest-battery), and he has even less of an advantage. I don't know Samus' biology, but MC is definitly had quite a bit of modification. If we include the books, he is generally more formidable.
Also, it would help if we knew the effects of Samus' and Iron Man's energy blasts on armor and shields.
Lastly, I think the most fun competition to imagine would be an all out fist fight.