The way I see it:
http://www.youtube.com/watch?v=ExWfh6sGyso
Replace "Romans with Cyrodiils"
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That's basically what the Septim empire did. New one, not much info.
The Empire as faulty as it is has directly thwarted Akaviri incursion throughout history. Skyrim's military has always composed a great portion of the martial might of the imperial soldiers. The loss of Skyrim either as a territory or ally would increase the existential threat of invasion, and don't forget that we ultimately only know of two non-Tamrielic forces: the Sload and Akavir.
My choice to go with the Empire follows both my personal desire to see an ascendent Empire again and the geopolitical realities that face Tamriel (probably).
The Akaviri are a non-issue, and have only invaded twice. Once was against Cyrodiil, and Reman soundly defeated them and integrated them in his empire, and the second invasion was in Morrowind, in which the Tribunal just flooded the place.
No, the biggest issue is the mer of Summerset Ilse rising to power. And as I've said, I believe this whole civil was in Skyrim is nothing more than a Thalmor conspiracy to get their enemies to kill each other, and attack when both sides are down.