Empire:
Still let the Thalmor walk around Skyrim freely.
Still banning Talos worship, which isn't the best thing for Mankind/ Let's the Dominion carry on with their plans of undoing creation.
The Nords are pretty pissed which is going to cause bother, seeing as they have a LOT of excellent warriors. (Possibly civil unrest)
The Empire will be spread thin(er) by having soldiers in Skyrim.
Stormcloaks:
Mankind is splintered/ divided.
Aggravates the Thalmor as they legalize Talos worship.
Possibly spurs the Dominion into motion, creating another war.
May cause a chain reaction where other provinces decide to rebel.
If the Stormcloaks decide not to become allies with the Empire, there may be a three-way war when tempers get high in the Dominion or the Empire.
So I ask, how do you think the War will pan out when the Empire or the Stormcloaks divide Skyrim? I think a whole Empire will do OK in the war, but then again if the Stormcloaks expel the Thalmor, then they won't have a solid foothold in the Empire, which is going to affect their plans.