Could they, under a just leader like Paarthurnax, who could have at any point durring the last 5000 years decided to embrce the old nature, but did not out of choice, not govern themselves and leave the mortals to do the same? Alduin was a fool. Paarth practically said as much. And when the Dragonborn returns to Nirn after defeating Alduin, all those Dragons flying around could have all descended upon him and ended his Saga. But they did not. One has even pledged to come when called.
If the Dragonborn is indeed the Talos of this age, with the benefit of the Dragon race returned to Nirn, he could lead Tamriel to a greater destiny than it had ever experienced before. Perhaps through his wisdom and strength he could bring about a pact between Dragon and mortal that will change everything.
The Blades heve been holding a thousands-of-years-old grudge. Alduin is what went wrong with the Dragons of old, but now it seems like they are being given a new chance. The gods did not intend one race to be superior to the other, else they would not have granted the Voice to mortals or the means to conceive of a shout like Dragonrend.
After defeating Alduin, the Dragonborn is asked what he will make of his destiny. Would he choose to be a force of good or eivil? It would seem to me that Paarthunax has the same choice, and he made it 5000 years before. Parthunax IS Alduin. Or rather, Alduin as he should have been. He has risen above his nature and embraced wisdom.
A pact between the new Talos and the Dragons might result in an agreement that each will leave the other alone. Perhaps the Dragons would depart Tamriel and go to one of the other continents of Nirn.
It's all just speculation. But at the end of the main quest, the Dragons are still there. The Empire and Stormcloaks are still at each others' throats. The Thalmor are still the enemy of the ideals of both. So the next stage of the lore is going to be quite volitile.

