I've been thinking about Marvel in the aftermath of Civil War, and the dichotomy between what we're being told, and what we're seeing. Quesada and Millar insist Iron Man's side was right, and Cap was wrong, but we see all this... morally questionable stuff the Pro-Reg side did to help their plans come to fruition.
Sometimes Iron Man looks like a hero (hooray!), like when he saved those hostages in Australia in his book. Other times he's lying about Cap being alive to trap his old friends, because 'it's the law'. Then he looks the other way while Warbird helps reunite Julia Carpenter with her daughter, even though Julia had lost custody, thus breaking the law.
The Initiative is supposed to be training inexperienced supers, but then decide to take away those powers (if they can, see that girl from the first issue of The Initiative) if the kids screw up a training exercise. All this while some former Nazi Scientist (or at least stereotypically evil-looking old German scientist) looks on, standing next to the poster boy for Government Jerkwards, Gyrich. Not to mention the absurdity of giving Norman Osborn a government position and control of a super-team.
Marvel is telling us one thing, but showing us quite another. So I'm wondering whether you think that's by design, or whether the guys writing these stories that seem to run counter to the company line are playing at being subversives.
I really wouldn't put it past Joe Quesada to stand there and tell us all one thing, while actually going a different direction with the books, but Millar seemed pretty insistent that Stark's side was "right". Of course, I base that on excerpts of comments he's made, that I've read on the Internet, where I can't read facial expressions, tone, or body language, so he could be joking around too, and I'd have no clue.
The other possibility is guys like Warren Ellis and Dan Slott are being told to write these books; they don't particularly care for the particulars of the assignment (Pro-Reg is right, Cap and his people just didn't get it), and so they're pitching things as part of the story on the grounds that they're "cool" and "edgy" (like that girl, Armory?, having her high-tech arm thing forcibly taken away for accidentally killing one of the other recruits), but really it's intended to undermine what the honchos have been saying.
I have to admit, the subversive idea sounds kind of nifty, but I think I'd prefer if Quesada were messing with us, saying things he doesn't believe, and that aren't true, just to rile us up.