With season 6 ending with Daenerys basically dumping Daario Naharis because she needs to be open to a marriage alliance, it’s quite understandable that some people might think that she and Jon might make a match to rule over Westeros. After all, they are both Targaryens (a family that’s notorious for their incestuous practices) so people wouldn’t be too bothered. Some would say that they’d be powerful together, riding dragons, defeating the Others, and binding the North to the South.
The thing is, it’s exactly because Jon’s been revealed as a Targaryen that works against this idea. Jon is a Targaryen, meaning that his claim to the North has literally been blown to bits like the Red Keep.
Jon has no claim to the North also because it’s not his father that was a Stark, but his mother, whose supposed abduction was the cause for the entire war to begin with. So when the Northern Houses realise that he’s not a true Stark, surely people will push for Sansa to become the Wardeness of the North (perhaps Littlefinger might even try to pit Jon and Sansa against each other, as implied in the season finale) because without a doubt some will be conflicted by the fact that he is a product of a union that caused the deaths of thousands of men.
Even though Jon doesn’t have claim over the North, he does have a claim over the Iron Throne. Let’s not forget that Melisandre said that when she looked into the flames to see the future of the Iron Throne, all she saw was snow. Technically speaking, Jon may even have a stronger claim than Dany, since Rhaegar and Lyanna might have been secretly wed (Targaryens sometimes had more than one wife).
Here’s when a Jon x Sansa union comes in. With Littlefinger being set up as an antagonist who will pester Sansa and bide his time until she accepts his hand in marriage, it would make sense that when she becomes the Queen in the North, she’ll have to marry someone for the sake of the Stark line. So if and when Jon and everyone else finds out that he’s a Targaryen, this makes him a worthy candidate for her husband. This isn’t just because he is really her cousin. With his claim to the Iron Throne and hers to the North, they would then have the right to rally the whole of Westeros to battle against the Whitewalkers.
Though I can imagine that Sansa and Jon will be reluctant to enter such a union, I wouldn’t be surprised that Sansa (as pragmatic as she is) will be the one to suggest the marriage. She trusts Jon and he trusts her, they love each other (though at this point in a familial way), and he is the only man that served her and stayed by her side because he cared, not because he was going to benefit from it (unlike Joffrey, Littlefinger, and Ramsay). On a side note, a Dany x Jon union just seems too cliché, having the “main” heroine marry the “main” hero. They are virtual strangers so there wouldn’t even be much personal conflict in their union unlike Jon x Sansa, who would most likely be torn over the fact that they were raised as brother and sister.
So to sum it up, a Jon x Sansa marriage would be politically more beneficial than a Jon x Daenerys marriage. Even if Dany were to have claim over the throne, she would have to secure the North’s loyalty via Jon (a Targaryen)’s marriage to Sansa, because they won’t bow down to a non-Stark once again.
We’ve got roughly 10 months ‘till we see what really happens. Jon x Sansa shippers, buckle your seatbelts.