The Civil War really needed a lot of things to be added to it:
Spoiler Defending/Invading multiple cities
Missions of espionage, sabotage, and subterfuge
Ambushes, sneak attacks, and sieges
Using diplomacy to win the loyalties of various Jarls, rather than just kicking them out and replacing them with a different one
And more. This would have actually made it interesting for me to participate in. I like zen's ideas for post-war random encounters too.
I also wish there was a side-quest/random encounter that allowed you to either help Talos worshipers reach a point of safety, or hand them over to the Thalmor. Maybe even helping them establish their own Sanctuary out in the wilds of Skyrim, similar to that one quest involving the Lincoln Memorial in Fallout 3.
It could even become a source of income for the player, earning gold for giving the head of either organization an Amulet of Talos or, in the case of the Talos worshipers, Thalmor clothing to take as signs that the Divines are on their side, and allowing the Thalmor to be killed.
All in all, I wanted both the Civil War and the Talos ban to have a bigger impact on the game than they seem to have had.