My thoughts are:
The Dragonborn is the start of a "new line" of Dragonborn Emperors much like Tiber Septim. I think not long after the Events of Skyrim, The Dragonborn unites Skyrim and sides with Ulfric Stormcloak, and The Dragonborn, Ulfric, with the help of Greybeards and Paarthunax reform the empire and the Dragonborn heirs rule Tamreil and the empire survives.
We know Ulfric Stormcliak knows how to use the Thu'um...as he was taught by the Greybeards....others can be taught...The Dragonborn could have an ailliance with the Dragons(since in game you can decide to allow Paarthunax to live). Paarthunax becomes the new leader of the dragons and sides with the Dragonborn....The Dragonborn promises Paarthunax and the Dragon peaces with men in return for aid against the Thalmor and helping the Empire....This also goes along with Ulfric, The Dragonborn, and the Greybeards teaching "exceptional men" in the army how to use the "Power of the Voice"...if Ulfric can learn how to shout from the Greybeards so can others...
The Dragonborn with the help of Paarthunax, the Greybeard, and Ulfric(teaching some of their men the Thu'um), and the Dragons Paarthunax brings over to "The way of the Voice", and Odahving (The Dragon the Dragonborn can summon) crushes the Thalmor and brings them back under control of the empire.
The Empire is reunited under a new line of Dragonborn emperors.....Ulfric Stormcloak is named the new high king of skyrim....and is the Dragonborn's second in command....
The Dragonborn Emperor's died out when Martin Septum sacrified himself to become Akatosh's Avatar to do battle with Mehrunes Dagon and cast him back into Oblivion....for 200 years the Dragonborn line was dead.....it was by the mercy of Akatosh seeing Tamriel was lost without a Dragonborn Emperor decided to bless an individual with the blood of the Dragonborn(you) to restore Tamiel.....
Long story short, The empire is reunified under the Dragonborn not long after the events of Skyrim....and he will have help not only from Ulfric, but the Greybeards helped Tiber Septim Too, and they hint the Dragonborn is not bound by their rules, The Greybeards will help indirectly by teaching others like Ulfirc "The way of the voice" and Paarthunax will aide the Dragonborn in return for peace among men...as Paarthunax and his kin will be under the Protection of the Dragonborn and his/her heirs moving forward(a covenent simliar to the one Akatosh made with Allesia will be made with the Dragonborn)
All will be well until...well im sure something else will happen, it always does....perhaps the re-emergence of the Aylields...afterall the Amulet of Kings has been destroyed...maybe they find a way around Oblivion being shut to them now that the Amulet has been destroyed...Oblivion does hint that there could be Ayleids still alive...hidden somewhere....could be interesting....who knows
