Well, to be honest I always had a sort of problem with Ellis' "Extremis" storyline in that while it was a good story in of itself, it should have remained pure elseworlds fodder because I never really bought that Iron Man would have done what he did. Tony as a character was always about human purity to a large extent, whether that's a failing or not is debatable, but it lead to him helping to develop things like The Sentinels. It's such a key personality trait that during the whole alternate universe "Earth X" storyline, Iron Man pretty much segregates himself in his enviromentally sealed building specifically so he wouldn't become a mutant, and works for a cure to the Teragin mists. Eventually he sacrifices himself heroically in a last ditch effort to stop the Celestrials (revealing the entire Stark Industries building to be a giant suit of Iron Man armor at this point), and dies the last human.
To me, "The Extremis" transformation, even if done with nanites/cybertech smacks heavily of human augementation, just done differantly than with chemicals or radiation, something that Tony would by definition rather die than do. I suppose it's something fans liked, but to me it never felt quite right.
It's sort of like how Batman is arguably the same kind of douchebag, he's a good guy, but he spends a lot of time thinking dark thoughts about metahumans, and how "humans were never meant to bow to a Kryptonian" in referance to Superman despite Supes never having given him reason to think that way, and oftentimes in response to Supes being a fairly nice guy.
It represents a sort of balanced counterpoint, being anti-super to an extent, without falling into the same extremes of say Cameron Hodge's crowd in Marvel. It also representing a sort of valid point of view from the perspective of "mere mortals" in dealing with what amount to posthuman gods. Someone like Tony or in DC Bruce, is in part defined by standing toe to toe with them without any kind of serious augementation. I mean either could have gone heavy cyber long before someone like Ellis' wrote Extremis, the fact that they didn't was kind of the point.
Warren Ellis is one of my favorite writers despite not agreeing with him about a lot of things, his run on "The Authority" and before it "Stormwatch" made quite an impression on me. I've even read his fiction like "Crooked Little Vein"... however I'll be honest in saying that departing from this one Iron Man stroy wouldn't be a bad thing, and to be honest I'm a little disappointed to see them using it, in any context, in the movies... to me it always kind of made Iron Man seem less like Iron Man, and his weakness of intolerance (to an extent) which lead to some very human mistakes like helping Project Wideawake helped make him a three dimensional character.
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As far as Iron Man having tons of suits of armor, that's kind of always been the point. Him controlling a bunch of them at once isn't something that has come up much, but arguably the quintessential Iron Man story has him getting his butt royally kicked, having to retreat to his lab, and then come back for a rematch with modifications or a new suit of armor intended to take down whatever he's up against. There have been plenty of images of Iron Man standing around with hundreds of differant suits in storage "just in case".
It's also noteworthy that Iron Man has also spent a lot of time developing armor for other characters, one example from back in the day was the "Guardsman" armor, with the guy using it acting as the warden of the original "Vault" which was Marvel's superhuman prison. The odd thing was that when Iron Man made armor like that he included an off switch, and it struck me as odd that when they did that whole Sentinels thing Iron Man apparently forgot to install one (if they ever came up with a reason why he couldn't turn them off other than not thinking of it, I don't remember it), something I felt was pretty hokey, though I suppose it wouldn't have been responsible for much X-men Drama if instead of a dark future the whole "Beserk Sentinel War" simply had Iron Man pulling the plug when things started to get stupid.