Dang, this is a long thread. When it comes down to it, both of these characters are a bit higher physically than humans. Their real durability, strength, and speed comes from technology. That being the case, the fight should come down to who has got the better tech (ie. dexterity, weapon power, durability, sensors)
Honestly, this fight seems really even (which explains why the thread is so long). I'm willing to give Samus slightly greater odds based on her supposed ability to absorb more damage. I give Samus 6/10, unless someone can convince me John 117's weapons have significantly greater power than Samus's.