When you play Skyrim you get an amazing RPG but its very black and white. Your the fabled hero and Alduin is the ultimate enemy. What if it didn't have to be that way?
Every story has two sides and if you can chose to kill an old lady with no more of a reason than you wanted their dagger why not more significant, game play effecting choices. Wouldn't you love to have the option to see a Skyrim completely different than the one you started with?
How about there is a man or woman, some next gen cultist who finds you in Whiterin after your fight with mulminiir and asks you to lend your ear. They explain who they are and why they need you. Really hit home that they and the dragons aren't the bad guys, merely rightful kings who have been usurped. Alduin was created by Akatosh to consume Nirn but he refused and took mortal kind under his wing and brought them into a golden age of advancement and peace (remember, all the ancient nord buildings are incredibly intricate and advanced compared to current tools) and in rage, Akatosh created the dragonborn, a being with the heart of a mortal, easy to corrupt and blind but with the power to destroy the immortal beings known as dragons. "You think it is mere coincedence that a dragonborn is discovered just as alduin returns? The very being that granted you your powers is the god of time, no there can be no mistake".
Then have the player make a choice as to whether they will join or not. From there you could get really creative, making NPC's with their own back-stories and reasons, side quests like recruiting or preaching, doing good or evil in the name of the dragons trying to get dragon worship normalised or at least renowned. Perhaps even crossovers with the other main campaign such as there being another dragonborn fighting with the blades doing the quests you would have done and its up to you to stop them.
So many directions you could take it in but I get ahead of myself. This would be a difficult project probably requiring a lot of work and code, not to mention voice acting. If you need any help with Dragon lore or the like I think I might know a group of people who could help out.
Anyway I hope you guys can make this happen!