There's actually a panel from shortly after Civil War, from the Iron Man series, where Tony says that, because he supported superhuman registration, both liberals and conservatives think he's on their side. He's says something like, "because I support the SHRA, liberals think I'll support gun control, and conservatives think I'll support the Patriot Act."

And that really drives home the point that the SHRA does not work as a direct analogy for real-world issues. If you want to just talk about the core Civil War series, maybe you can make a good case that it's supposed to mirror the Patriot Act, but the more tie-in series you consider, the muddier the analogy gets. I don't think the writers of all the different tie-in stories agreed on what the SHRA meant.

I agree with the other commenters that -- although one side lost and one side won -- neither side was supposed to be "right" or "wrong".

I will say that I can not reconcile Tony's actions in making a mindless clone of Thor as a weapon with the Tony Stark who, you know, DOESN'T MAKE MURDER CLONES OF HIS FRIENDS, so I usually pretend that never happened. Ugh.

I have been rereading the Iron Man: Director of SHIELD run lately, and I do think some of the political messages of that are a bit disturbing, such as: you should let SHIELD invade other countries even if they have no proof of the WMDs that they say are there, because Tony Stark knows everything. Even if he has no proof.

I didn't mind the plot so much, because Tony and SHIELD have always been morally gray, but I didn't like that, after the fact when Tony had gotten proof by disobeying orders and invading other countries, the public response was, Oh, never mind then! You're our hero again! That did feel like it was justifying the lack of proof (or the fabrication of proof) of WMDs.