Stormcloaks. Now I DO hate their racist attitudes (I pretty much exclusively play Dunmer in Elder Scrolls games). BUT, I read the Nu Mantia Intercepts and the Altmeri Commentary On Talos. Both amazing pieces of deep lore regarding the metaphysical nature of Nirn and it's existence.
For those not in the know, the elves or "Mer" believe they are descendants of the "Aedra" or "Ancestors", their name for the Eight Divines. Men on the other hand are usually referred to as The Sons Of Lorkhan.
I won't go too deeply into the creation of Nirn, but each race of Mer attempted to raise themselves back up to godhood by creating or controlling Towers. giant structures connected to "Stones". There are also some Towers which are not raised by mortal hands like Red Mountain, Adamantine and Snow Throat but the others such as Orihalc, Crystal-Like-Law, Walk Brass and White Gold are mortal made and act as manipulators of Majika, or, due to the Wheel Within A Wheel nature of White Gold, Creatia itself.
Now, these towers also have another, possibly unanticipated effect, they stabilize Nirn's space and time as a bubble within Oblivion and Atherius. It is because of these towers that the world exists at all.
For example, Adamantine's stone is called the Zero Stone or Convention. It is where the remaining god's met after creating Nirn to punish Lorkhan's treachery and in doing so, Akatosh created a point of reference that began linear time in Nirn, Lorkhan's heart landed in the sea and became Red Mountain but this tower's effect gave Nirn it's own, special kind of divinity which let the Divines leave it without it or they becoming unraveled. So, Adamantine stabilizes Time in Nirn, and Red Mountain prevents it from unraveling.
But what does Michael Kirkbride's rambling lore have to do with the Stormcloak, Empire conflict you ask? patience, I'm getting to that.
The Thalmor wish to return to being the gods that they believe they are descended from, but nowadays nobody knows how to raise themselves up through use of the Towers, and in fact, the Thalmor have found another solution.
They wish to unmake Nirn.
Over several games, towers have been falling. Numidium, Walk Brass, was deactivated in Daggerfall, Red Mountain in Morrowind, we saw what happened when the stabilizing effect of White Gold was temporarily deactivated during Oblivion and Snow Throat in Skyrim may have been deactivated depending on what it's Stone was. Crystal Like Law was destroyed by Daedra during the Oblivion Crisis and Orihalc was destroyed when a Redguard sank the island by performing Prankatrosword. The great, walking tree city of the Bosmer has stopped moving after the Thalmor took over their woods which may indicate deactivation as well.
The bars that hold the world together are coming apart, and the Thalmor are getting closer and closer to their goal. They wish to remove Talos, a mortal made god, from the Mythic and thus weaken Nirn further, hence their banning of his worship, they also wish to not only kill humans, but remove the very idea of them from the weave of possibility so that the Sons of Lorkhan cannot act to stabilize the world's divinity with their presence.
Thus, I side with the Stormcloaks. If Talos is removed from the Mythic then all of Nirn is in terrible danger. and may be dissolved back into Atherius.
Nu Mantia Intercepts: http://www.imperial-library.info/content/nu-mantia-intercept
Easier info on the towers: http://elderscrolls.wikia.com/wiki/The_Towers
Altmeri Commentary on Talos: http://www.imperial-library.info/content/forum-archives-michael-kirkbride
More info on the towers: http://www.uesp.net/wiki/Lore:The_Towers