STOP WITH THE STUPID NUMBERS.
Since you seem so obsessed with them, here are some somewhat less biased numbers, based mainly on ability:
Master Chief: 6000
Mega Man: 7000
Samus: 7000
Samus and Mega Man both have strengths and weaknesses, and these happen to balance evenly (Mega Man may be more powerful at some point, but the whole "spikes" thing kinda sucks). Master Chief is powerful, but I wouldn't put him up there with the other two.
Even though they have absolutely nothing to do with this argument, here are my numbers for some other stuff, just to make a comparison:
Roll: 2750
The Metamo Ark: 6000
Isaac (from Lost Magic) with access to every rune: 3500
Warp Rattler/Vic Viper: 6500 (it would be higher if it didn't suffer from OHKS, though it could probably take out Samus and Mega Man at the same time if it was properly shielded, had 4 options, and had piercing lasers)
I'm not saying I'm right. In fact, I'm probably quite wrong, and I'll have people jumping down my throat because my numbers don't match up with theirs. However, I'm just trying to be as fair as I can be here. Again, this is pretty much based on ability, not on how much I like them or how awesome they are.
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