Round 1 - Given that these are merely empty robotic suits, Thor nukes them. He shouldn't have any moral problems with trashing a bunch of Tony's suits. So round 1 is a stomp. It was pretty evident in IM3 that Extremis easily matched any of Tony's Iron Man armors. Nearly every time a suit was shown in single combat with an Extremis soldier, the suit lost. Even when Tony was piloting the suits, he he burned through 3 or 4 of them fighting Killian. Even Pepper Potts was able to fairly effortlessly dispatch a suit at the end of the film.
Problem is, Thor has no way of knowing there are nobody in the suits. I'm depending on Thor's morals, since he will think people are in the Iron Man suits and hold back a lot against them, possibly resulting in him being ganged on and a possible KO. The Extremis can heal though, so that is an edge they have against Thor, so you can't really compare them. Tony going through 2-3 of the Iron Man suits was just part of the movie to buildup to the climax, since Tony could have just flown in the air and spammed his energy attacks against Killian. But I suppose, if its morals on, it could end the same way. Iron Man has already displayed he can hang around with Thor for an extended period of time, so Tony with backup could take down the Norse God of Thunder.
Round 2 - Captain America is the only one that stands a chance in this fight. And given that, 50 Extremis soldiers are too much. Tony got tossed around every single time he went toe-to-toe with an Extremis soldier. Extremis made the soldiers stronger and faster than the Iron Man armor, and on top of that, Extremis soldiers could burn straight through metal just with their touch. While potneitally quicker in combat, Cap is most likely no where near as strong as Tony's suits, and additionally, he can neither fly (like the suits) or would he have any way of significantly damaging the Extremis soldiers. Hawkeye could potentially use explosive arrows but even then, that would be hit or miss in terms of lethality. Killian was able to shrug off the self-destruct explosion of the Mark 42 armor and Pepper Potts was able to fall 200 some feet into an explosion without any signs of damage. Black Widow's pistols would be useless. He electric gloves may be useful given that it was shown in IM3 that one Extremis soldier was presumably killed by a combination of an explosion and landing in power lines. However, to use her electric gloves, she would have to engage in hand-to-hand combat with an enemy that would be faster and stronger by a wide margin.
I think Killian and Pepper Pot had lots of plot shield. Killian's right hand man Extremis bodyguard was killed in one energy blast to the chest while Iron Man and him were duking it out in the airplane, so if these are just fodder Extremis supersoldiers, an explosive arrow from Hawkeye would take a couple of them down, and that's just one arrow. Captain America could buy them more time by swinging his shield and knocking them back for Hawkeye to keep his distance and unload more explosive arrows. Black Widow could also hold them back and distract them, or even have a little strategy to take some out (I mean, even Rhodey managed to take down a couple of them). Sure, Natasha is not nearly as strong as any of the Extremis supersoldiers, but she is pretty fast and agile to hold her own and use her electric gloves. Also, Rhodey managed to knock back the Extremis supersoldier when he was forced out of the Iron Patriot suit, so its not impossible to take them down. She's tanked a hit from Hulk before, so I don't think she's a non-factor here.
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