My main theory, though, is that they seem to be making a point of comparing the player's character to Tiber Septim throughout Skyrim and, if the Dragonborn is to follow in Septim's footsteps, they will lead to the formation of a new Empire.
Also note that Hammerfell, Elsweyr, and Black Marsh have all seceded from the Empire. (Along with the Summerset Isles and Valenwood, if you choose to count forming the Aldmeri Dominion as "secession".)
Combining these two things, TES6 will be able to say "the Septim Empire fragmented and several provinces seceded before it was reunited by the Dragonborn". By not stating whether Skyrim was one of the seceding provinces or not, they avoid any need to state any particular result of the Stormcloak rebellion.

