For the first expansion I'd like to see the whole Thalmor issue resolved, with significantly different plots and events depending on whether you sided with the Stormcloaks or the Empire. For example, a newly-independent Skyrim could be forced to defend against a Thalmor invasion, and mount small, guerilla-style attacks on the Summerset Isles (my preferred choice of location for DLC) in retaliation.
Alternatively, a newly-united Empire could decide to put an end to the unfavourable conditions of the White-Gold Concordat by taking the fight to the Thalmor - first a rapid and crushing invasion of the Isles, and then maintaining an occupying force there.
In the Elder Scrolls lore it's occasionally stated that the isles have a problem with attacks from the Sload. The expansion could use this (and build on it) to get around the major problem with the idea - which is that the Thalmor would be drastically more powerful than a wartorn independent Skyrim or the nigh-crippled, albeit still united, Empire.
Supposing one joined the Stormcloaks, news of a crushing Sload offensive launched on the Summerset Isles after the Thalmor attackson Skyrim began would explain why the Nords haven't yet been steamrolled off the map, and make the idea that Skyrim could repel their invasion more viable.
If the same news were to reach the still-united Empire, they might take it as an opportunity to forcibly re-negotiate the terms of Concordat - that is, by invading, conquering and forcibly incorporating the Summerset Isles into the Empire.
Both plots could use the same assets and areas and offer a wide variety of mission types beyond the usual "go here, kill everything" type, but they could still be wildly different and worth playing from both perspectives. Hell, I can think of at least a half dozen completely new (to Skyrim) quest objectives that could be implemented without requiring changes to the game's mechanics, so who knows what Bethesda could come up with.