One thing that gripes me is in the SHivering Isles, you basically became the Lord over a land. I doubt very few players actually opposed this happening and it made characters who wanted o be great leaders or Kings a spot in the TEs series by handing them over this Daedric Realm. However, I dont see why this could not have been done in SKyrim. Skyrim's Nord traditions open up for two possibilities:
1. The idea of fair combat in challenging the High King
2. The advancement of the Jarls through war
One thing I thought was really weird was how the Jarl of Whiterun is chosen on the Stormcloak side, if a stormcloak victory.
The second idea is that the PC could become High King of SKyrim. What is made clear is that there is a tradition in Skyrim where the High King can be challenged to fair combat for the throne. On either sides case, should the PC have been made a Jarl, the PC could have been given an extensive questline (Possibly through Hadvar or Raolof) to gain the favour of either sides army, in order to gain support to take the position of High King. This would have allowed for more endings to the civil war then the ones given, and presented the PC with more possible choices.
The second idea is not in itself outlandish because, looking at the civilizations that the Imperials and Nords take after, the idea of raising a high ranking military leader did happen. Culminate this with the fact that the PC is the Dragonborn would give him much sway among the Nords as a "Hero". Talos himself was a great general who became the first in the Septim line. I dont think its a stretch to say the civil war could have been a longer quest, allowing the for PC to choose between being a Soldier and a Leader. While the game is already out and its a bit late to consider these possibilities, maybe this suggestion might inspire some modders or even Bethesda to expand the civil war through a DLC.
Just some food for thought on the potential the civil war could have had

at least with the thieves guild you werent the only one chosen for the final honor.