I dont think Stark was necessarily portrayed as "evil" in CW , or that his side of things were misrepresented in ideology . That kind of things comes earlier in stories like the Crossing , or later in post CW avengers/iluminati stories .

I think that it's just so much easier in book ultimately about superheroics , to relate or agree with cap .

We can see the Registration Act as an allegory for the debate of giving up civil liberties for the sake of safety and security. A pivotal question asked by the books are: "how much freedom are we willing to give up in order to feel safe?" The Iron Man camp suggests that nothing is more important than the safety of the state, even if that means limiting the rights of of citizens and on discriminating and removing rights of certain minorities. The Captain America Camp suggests that we cannot deprive ourselves of our natural born freedoms simply for the sake of national security.

There is little way that any hero leading the pro-reg side would come out the most popular , and not look like a governement stooge , when juxtaposed to the beacon of freedom and strong moral fiber ...

Tony still had a massive chance to shine , and show the pros of his décisions .Tony's argument is a logical one: the only, ONLY organization actually training people how to use their abilities in an ethical way were the X-Men of all groups . The Avengers, the FF, SHIELD, etc. No one had a training program designed to do that. Tony's plan to do that and to develop a peacekeeping organization designed to provide greater protection to civilians outside of the New York area made a lot of sense, since we know that bad guy organizations clearly exist and are active all over the place .

And it clearly worked , the Initiative was a pretty good idea and efficient . Even if of course the next status quo changes turned it around in Dark Reign .