He's got his suit colored dark blue/black around his neck. And on the powers subject, I think the way to go would be some kind of mixture with Ms. Marvel and Luke Cage (or Thing). You can mix animations from up to 2 characters, right?
Yup, you're right. In fact, checking Mighty Avengers #1, the cape is the only blue part of the costume, I'll darken everything else later for Mighty, the other two, I like them that way.
I'm not really sure of what to do or with the powerset or how, I'm still in the trial and error stage. I'll work on that after trying the models that iammingy and BliZZ suggested (and finding Ult. Thor's offsets).
EDIT: The cape bolton wasn't so hard, and it moves and anims OK, without the white outline from Magneto's. Now comes the hard part: reskinning Thor (and hope those blue circles are just painted and not a separate part of the model).