One of the problems seems to be, in Elder Scrolls VI (assuming there is one), the whole Empire vs. Aldmeri Dominion thing will matter (who wins, how the Empire looks by the end of it, etc.). If the Dragonborn were to become Emperor, the shape of the Empire would depend entirely upon the choices undertaken by the Dragonborn in Elder Scrolls V. For example, a Dragonborn that fought for the Stormcloaks (one possible explanation would be a popular uprising in the Empire that reunited with the Stormcloaks against the Thalmor... or the Stormcloaks could invade Cyrodil and install the Dragonborn as the new Emperor). If the Dragonborn were to back the Imperials, he would only be extending the rule of the Mede dynasty (assuming he didn't lead some coup or popular uprising himself... or the Medes could die out with Titus Mede II and the Dragonborn could be named his successor).
Of course, there's a pretty big problem if the Dragonborn joins, say, the Dark Brotherhood and murders the Emperor.
I'm of the opinion that future Elder Scrolls content should focus on the conflict between the Aldmeri Dominion and the Empire (... and the independent kingdom of Skyrim??? A problem for future content is how this works out canonically; given that the Empire is already collapsing, independence could be inevitable?). If that's introduced as a DLC or something along those lines, we don't need an Emperor Dovakiin in order to participate.
I think that Titude Mede will die either by the Dark Brotherhood, or for another reason (assassination/natural death). The Elder Council will catch wind of the Dragonborn being alive and in Skyrim and could possibly be sought to bring the empire back to Septim's glory. If the player sided with the Empire, Tullius can verify to the council that Dovahkiin is a capable legate and can take control of the crumbling empire. If sided with the Stormcloaks, then Ulfric's Skyrim feels more confident with an empire lead by one of his own generals and the dragoborn (which is how Talos got Skyrim's backing) as long as the worship of Talos is reinstated (both choices will result in the Second Great War either way).
Also, I don't think Dovahkiin's destiny was just to kill Alduin and save mankind (because the Dragonborn can be any race) but have the Dovahkiin fight against the Thalmor to bring peace again to all races. This can be ambigous and successful. Skyrim's future as a game has serious potential to be even more epic and grand, and the peace meeting shows that the dragonborn can handle political dealings for which he/she favors.