Sorry about the delay in the reply. It’s cool to see people interested in this.

[@RedXIII]
So I as the GM would control all the canon Avengers, but they will mostly be relegated to the role of side NPCs. The players’ original characters will mostly work autonomous of the other Avengers as they are now spread out across the globe. As for story structure, I do envision it being primarily mission based, but also having periods in-between missions in which the players can do what they want to advance their own stories. I would also collaborate with players to work their subplots into the missions. Hopefully that answers your questions.