I root for the villain usually when they are a sympathetic character or their actions are somewhat justified, or when the hero really isn't any better. Casting them against an even greater evil works as well, as does making them seem not completely evil.
I am far more concerned about what Thor Odinson is doing. We haven't seen him since he fought the Beyonders. They need to tell us what is up with him. I don't know if I am buying The Mighty Thor. If it has Thor Odinson in it then I will, but otherwise I'm probably not. This is a Jane Foster story at this point.