Probably been said before.
I want a Thalmor Invasion, full scale war all centered around Dovahkiin and the Empires/Imperial refusal to give him/her up to the Thalmor.
Skyrims engine can handle quite large fights (30+). I would want to see the entire north of the map to spawn Thalmor camps, raiding parties, and huge skirmishes. With intermittent raids on towns/cities.
The plot should call for Dovahkiin to lead a small team on a precision strike against the Thalmor, perhaps capturing a leader, and therefore bartering a truce.
EDIT: Some more ideas.
The plot could have different options for different types of characters to resolve the war in ways they see fit.
Examples,
An assasin char could choose to take a contract to assasinate a thalmor leader in order to help the war effort.
A mage could work with the college to create a magical barrier to keep the thalmor out, lore wise it would work, as there is magic to counter oblivion, vampires etc, why not thalmor?
A pure warrior would have big bloody battles for much skullbashing.
A thief could choose to take a much more clendestine approach. For example, working with alchemists to create a powerful poison and distibute it in a thalmor city....
This kind of choice... would be amazing. Could all be done with a single landmass addon too.
All of these could include some or all of the various groups within skyrim, eg Mages College or Companions.