What are the main military factions within all provinces in the current timeline?
Skyrim - Stormcloaks, Imperial Legion, Forsworn

Cyrodill - Imperial Legion, any others that i missed?

Black Marsh - Ah-Xileel, any others that i missed?

Morrowind - Ah-Xileel, House Hlaalu maybe? House Telvanni maybe? any others that i missed?

The Crowns and Forebears in Hammerfell. Elsweyr also has Anequina and Pelletine, although I'm not sure if they count since they're both under the Thalmor.

Also there's still a lot of political intrigue in High Rock, possibly between Daggerfall and Wayrest although this is speculation since Wayrest was apparently sacked by corsairs.

The Imperial Legion would also have a presence in High Rock and Morrowind.

Don't forget that Cyrod has the Specialized Memomancer Hacking Strike Team, fighting the Thalmor in virtual unspace of dreaming dead waiting for their attempt to realize their lucid dreams as to invert the progression of the countings of ancient numbers and alphabets as to fall past the bottom and end up at the top. Soon, they shall break the spectracodes as to enter GREATTHALMOR/OS to topple the govern-ments of Alinor forever until the next AD.
[/monkeytruth]

That kinda reminds me of the stormcloaks and imperial legion, i wouldn't mind having the next game set in hammerfell. Was really about the crown and forebears and it turns out there is a third major faction in hammerset so a 3 way battle instead of the two way in skyrim.

IIRC Sentinel was neutral, so it might be the third faction you're looking for.

Hammerfell also has the Lhotunics, which were developed after the Warp in the West, I believe. They're sort of the middle ground between the Crowns and Forebears.