My character is at lvl 49 now. I did

* Thieves Guild, including "restore to former glory"
* Companions
* Dark Brotherhood
* Stormcloak campaign
* lots of mini campaigns

During the main quest, I talked to the Dragon on top of the mountain where the Greybeards are. My current quest is, to learn about the location of an elder scroll.

What I miss:
Besides the quest to infiltrate the Thalmor embassy I can just hunt these racist zealots with no influence to the game. I know, that there is something during the mage guild quest line, but that's only a single target.

My question:

Is there a quest in which I can destroy the entire faction for good?

Nope, but that would be an obvious choice for some DLC!

Oh my god, how I'd LOVE to have a Great War expansion / dlc!

Charging into battle with Ulfric Stormcloak / Imperial army / (enter your favorites ^^) and putting Wuuthrad to use because it's "Especially deadly to elves" x)

They seem to be set up as the big threat for the entire era. I wouldn't expect to be able to destroy them for another game or two.

Hmm... although I've been playing all Elder Scroll games, I never dived deeply into the lore, so I don't remember the Thalmor from earlier games. Did I just forget them?

It's been 200 years since the last game. It's a new era. Some things have... changed.

Not that I've found. Although if you do find a way to Summerset Isle and/or Valenwood, I'd sure like a heads up.