We cant just fight dragon through the whole main quest so who will be the soldiers that you fight. Im leaning towards whichever side of the civil war that you side against, but it could also be dragon cultist or somthing.

Hopefully what with all this radiant story and such we'll be able to choose our own side in the civil war. I'm hoping for something at least on New Vegas's scale in terms of paths through the MQ.

Hopefully pro-Imperials on Skyrim's civil war

I'm anti-imperialist thought and thought. Although I don't know if that would conflict with the MQ, or with being a Dragonborn, or whatever (I hope it doesn't).