We could also opt to keep Tony Stark in place. He has broadcasted his message which has gotten the appropriate response. The resistance does not really need an overall leader after that. I think that in the seperate sections several characters will take the leadership or front runner role; or that might change depending on expertise. For example, I can imagine Magneto letting Cap do his thing in NY (as long as it coincides with Erik's interests) in most decisions, somewhat similar to the working relationship he's had with Xavier even if this one isn't based on friendship. But where research of the vial comes into play Magneto wouldn't defer to anyone. He knows best (or so he thinks. In this case it might even be true)