That being said I have 0 faith in Elder scrolls VI and Bethesda will probably make the Dragonborn join the Imperials as canon

In the past, Bethesda has done a good job in the Elder Scrolls games of spacing things out enough so that there's no real decisions from the previous games impacting the future games. See the Nerevarine just vanishing and then Morrowind blowing up, or the Warp in the West.

In this case, though, I'm not sure. Even discounting the politics, what they've done in Fallout has majorly soured my opinion of them. Given their apparent massive boner for "everything must have Brotherhood of Steel, all the time!" I could easily see that being translated into "There must always be an Empire!".

The logical continuation of the storyline, though, is the Empire disintegrating (regardless of Ulfric), and then TES VI being rebuilding something from the ashes of it. Somerset, Valenwood and Elsewyr are under the control of a hostile, foreign power. Hammerfall got abandoned by the Empire. Morrowind is in chaos and ruins following the eruption and Argonian invasions. And Black Marsh was never really that integrated with the rest of the Empire to start with and broke off to do its own thing following the Oblivion crisis. That leaves the "Empire" holding:

Cyrodiil - still recovering from the Thalmor invasion High Rock - a historically problematic province full of power-hungry nobles Skyrim - in open revolt

Even if Ulfric gets put down hard and Skyrim fully bends the knee, the Empire is doomed.