They're not both being marketed as villains. It's pretty clear what we're seeing here -- a conflict between their methods and ideologies, and what they stand for. They are both individuals who are not only in conflict with one another, but they are also in conflict with society. They both realize the potential danger of one another should they choose to use their "abilities" or methods to cause serious harm to the public.
But even Perry White tells Clark "You don't get to decide what the right thing is". I think they're setting up the idea that neither Bruce nor Clark is 100% right in how they're approaching certain situations.
Exactly, and that's part of what's interesting to me about their conflict. All of us and the movie's viewers will know that Batman and Superman are technically "good guys". The both mean well, they want to protect innocent people from harm, even if they go about doing so in different ways, and I'm sure the film will make this clear.
But as you said, neither of them are 100% in the right and they each seem to have some issues. Is Superman not being a hypocrite here? Is he right to think that he's above us and gets to decide "what the right thing is"? After all this Batman has been through (including the death of a Robin), is he right in being so distrustful of Superman? Have his methods become too extreme over time? Will he realize that he no longer has to be a "one man" army and learn to be trusting enough to fight side by side with someone again?
Obviously, we have a pretty good idea as to how those questions will be answered and what the outcome will be, but it'll be interesting to see how they get there.
Part of what intrigues me about this conflict are the motivations and ideologies in play here, including Lex's. Rather than the typical superhero fare featuring a hero facing off against a villain bent on causing chaos and destruction or gaining power, each of these men truly believe that what they are doing will make the world a better place, including Lex it seems going by the viral marketing and interviews with Eisenberg. The "right and wrong" here isn't exactly so cut and dry.