This is purely conjecture, but here's my version of events after Oblivion:

With the Imperial line finally and officialy severed, the provinces will see it as the perfect excuse and opportunity to secede back into independent states. Three nations ceize the chance immediately: the Altmer of the Summerset Isles (they've always considered themselves higher than other species, plus rumors just before the Oblivion crysis said that "syndicates of wizards are leading a boycot of Imperial goods in the Summerset Isles" - those same syndicates will lead the liberation effort), Vardennfell (hope I spelled that right, we all saw just how much the Empire is despised there) and Skyrim (who have always been the boldest when it came to shifting borders). In a desperate effort to maintain as much stability as possible, the Empire revises its government system to give the Council (who were the active government during the crysis) full governance over all aspects of rulership that previously belonged to the Emperor, effectively turing the Empire into a federation. This backfires however, as many see this as opportunistic usurpation, not helped by the fact that the Council's members were, at the time of the crysis, decided by who had the most wealth (those who read "A brief history of the Empire" will remember that one of the Septims disbanded the Council and forced them to buy back their positions). Ultimately, the Empire cracks down into the new rebel states and what is left: Cyrodiil plus a number of regions that the Council managed to hold. This, of course, does not go without bloodshed, as the Imperial Legion and rebel clash in various battles. Though the Legion is a powerful military arm, it suffers many losses simply due to the fact that their forces are stretched thin between 6-7 different states. Eventually the battling reaches a stalemate, and after nearly a decade of fruitless efforts, the Council finally lets go of the lost provinces, focusing instead on those it managed to keep. This does not mean and end to hostilities however, with skirmishes, bloody clashes and incidents frequently occuring along the war-torn borders. This continues for a century and several decades, and even after all this time the hatreds remain. Eventually those hatreds grow into xenophobia. Having over 100 years to rebuild their forces, Skyrim and Vardennfell come to realize that their age-old nemesis has had the same amount of time to gear up to retake what the Empire lost. Fearfull of this push, they decide to strike first. Some say that the leaders of both states agreed to strike at the same time from diferrent fronts at once, but official history states that each invaded various regions of their own initiative. The invasions end in disaster, as the Nords and Dunmer are faced with powerful fortifications along the borders, set up by a Council well aware of how big a threat they posed to it. They attempted to lay siege to them several times and failed miserably every time, losing many men in the process. Thus the invasions ended before they even started, and after a few years of more bloody fighting along the borders another stalemate is reached. This grand failure isn't taken lightly in the invaders' states, the lords blamed by the populace and each other for wasting countless lives and resources on a foolhardy war that no one really wanted. This resentment turns most sour in Skyrim in particular, where the proud Nords savor the least fear of the ruling aristocrats. Protests, boycots and outright violence ensues as a result. It takes the thanes much effort to quell the uprisings, effort that involved terror and repression. Though for a time Skyrim was at peace, the people did not forget these attrocities, and started banding together into new factions to get back at their tyranous rulers. Over decades, these factions grew in number and power, and, subsequently, boldness. They undertook various shadow operations to hamstring their oppressors: assasinations, sabotages, subterfuge... With each year, there are more and more rumors of people suddenly going missing, goods disappearing, arsens of mansions and military operations turning ugly. Everyone knows who did it, but no one can prove it. But they try, and the accusations fuel much anger. This all continues until finally, someone crosses the line, and it's the last straw - the hostilities turn first into violent conflicts, then escalate into civil war.

... whew, now that's a long post . Sorry, bu you got me going

Also, here's a quick summary of the conditions of the provinces at the time of the novel (the ones the books mention, anyways, which doesn't include Skyrim).

-Cyrodiil: recently reunited under Titus Mede.
-Morrowind: decimated when the Ministry of Truth finally was released from Vivec's spell. Many Dunmer migrate north to Solstheim.
-Blackmarsh: independent. Expanded to include southern Morrowind, which the Argonians invaded in the aftermath of Vvardenfell's destruction.
-Elsywer: after the Mane is assassinated, the province falls apart into a bunch of minor city-states and nomadic tribes.
-Summerset and Valenwood: Summerset conquers Valenwood, forming a new Aldmeri Dominion.

I hope the novel's sequel will mention the Redguards too. Apparently they're playing along with Mede's empire for now, but I got the feeling their participation in the empire is half-hearted by that time (40-some years after the Oblivion Crisis).

If they'd add the kick from Dark Messiah I would love to join the pro-Nord faction, throw that kick at Imperial Legionnaires and roar: "THIS IS SKYRIM!!!"

^{(Or I could stop dreaming.)}