It looks like the "new" empire is run by usurper.
-They're banning the cult of Tiber Septim
-Blades are outlawed
-Aldmer agents are helping the empire taking care of rebellins despite this is not in the best interest of a foreign power which was recent at war with the empire.
All this leads to:
A ) Stormcloaks, indipendentist and probably distrustful of Aldmers and new empire motives
B ) Septims supporters, worshipper of Talos and some part of the legion (Blades and who knows) still loyal to the old empire
C ) New empire, agents of the Dominion
Probably at some point A+B will make an agrrement to combine forces against C. Player, as a Dragonborn, will be a pawn in the grand scheme of things.
I'm sure the new Empire banned Tiber Septim and outlawed the Blades because of their connection to the Septims. They don't want people to worship the Septims because they want to be recognised as the new rulers and not constantly be under the shadow of a previous dynasty.
Now, the Thalmor helping the Empire is
not necessarily not in the best interests of the Empire. If the Thalmor can be used as allies and they serve their purpose, they would be helping the Empire and that would be good for the Empire, so long as he Empire makes sure they don't sabotage them or anything.