That's the thing right there, I have played DC Universe Online for a very long time because after playing Champions Online I quit the game and started playing DC Universe Online. Every single "Hulk" I seen has never gotten a report from a player. Every friend I have in there whose character is based off an iconic character (Capitan America, Wolverine, Iron Man as you said, and so on) that are not DC Comics based have never had their account banned or suspended, and some of them have their account full of iconic characters, meaning everything time they jump in the game they are playing on an iconic character
None of that matters though. Those players signed an agreement. They are now in violation of that agreement, which means they are no longer permitted to play the game (that's what the agreement says). Just because they have not yet had that punishment enacted does not mean that they won't eventually or that it's okay.
Now this is the two main things I do not understand and also the main things that has me confused with all this copyright stuff, how DC Universe Online get away with it all and Champions Online can't
What you aren't understanding is that both games are doing more-or-less the same things to proactively try to defend themselves against IP litigation (they are probably doing more behind-the-scenes in terms of deals and communication that you cannot see). You're only a player of those games, you are given extremely little insight into what's going on within those studios in the operation of those games. Just because you have never personally observed (or heard of such an observation from your friends or community) such a ban doesn't mean it hasn't happened. It just means you haven't seen it. Perhaps DCUO has a more subtle internal policy for dealing with the situation. Perhaps they are just collecting a large list of accounts to ban and will do them all in one fell swoop at some future date.
Even they legitimately have not done anything to ban IP-infringing characters yet, they have still put themselves in a position where they can trivially do so if they need to.
If you are really set on creating this game in the fashion you originally described I strongly advise you to hire a lawyer, preferably one with extensive experience in IP law. Your own understanding is dangerously flawed and could result in years of work down the drain in some cease-and-desist or (worse) litigation. Don't risk your time like that, it's worth too much.
