It does make sense.
I've felt for a long time that the next game in the series could almost be a 'semi-expansion' of Skyrim/Oblivion along this theme, sort of like 'TESV and a half'.
As it stands, if a player follows the sequence that I have, it's an almost logical progression to that end. The people and leaders of Skyrim see the pc as a person to be reckoned with, a real legend come to life type, plus the dragons all know him/her as the defeater of the world-eater, and some of them are swearing fealty, plus the pc has an (albeit limited) control over them. I tend to think that both the Stormies and Legion would be seriously weakened if a pc dovakhin raised the banners, although I'd also suggest that perhaps one or the other of Ulfric or Tullius would have to die...my money would be on Ulfric, as swaying Tullius to your side would assist in swinging the non-Skyrim troops and Legions over to your side for the march on the Imperial City and, ultimately, either the war with or occupation of the Thalmor lands.
Personally, I'd give the Thalmor the opportunity to step down and accept one of two options - either they surrender government of the Isle to a more 'pro-empire' group, or they maintain government under Imperial oversight. If they didn't want to do either of those, I'd offer the dragons the Somerset Isle as land of their own, if they laid it to waste...any survivors would be welcome as part of the empire so long as they swored fealty to the Emperor and settled in Empire territory. Those who lived on in a ruined Mer land would soon find out what dragons can be like as overseers.