they both were smuggled as infants after the deaths of their mothers, just because they were targaryen babies born at the end of robert's rebellion, mr. "my throne rests on children's corpses" baratheon. but while jon was moved from the south to the north, dany was taken from the west to the east. they both have journeys deeply rooted in the lands of their ancestors, jon went even further north and beyond the wall, while dany moved even further south, in the deepest parts of essos. both actively worked on correcting their ancestors' wrongdoings, jon on the survival of the free folk who were left beyond the wall by other first men (that became northern lords of westeros later) and dany on the abolition of slavery (that the valyrians picked from the ghiscaris and spread across essos).

and both of them acquired the original magic of both continents, warging in westeros and dragontaming in essos.

granted, dany's feat is simply grander: she brought magic back into the world as a whole, and dragons are key to defeating the others aka saving the world. in comparison to her hard work on birthing her dragons, starks seem to have their direwolves being handed to them on a platter. still, i think it's both beautiful and neat that it's jon, not anyone else, who persuaded ned to take the direwolves in the first place. not to mention how direwolves disappeared from the seven kingdoms not long before the death of dragons. and then they reappeared in the beginning of agot, right before the return of dragons in the end of agot.

it's quite clear to me that they're going to meet when they will eventually go back, jon to the south and dany to the west, to join their forces and their magic to defeat the great threat to humanity, the main plot points of the series that they're strongly tied to.

after all, we know that

"To go north, you must journey south. To reach the west, you must go east. To go forward, you must go back. To touch the light you must pass beneath the shadow."

Washes of Light