The bad: Even if neither of them realizes it, Jon and Daenerys are pretty closely related. We know that incest isn't out of the ordinary for Targaryens, especially in nonsibling relationships, but there's still a creepy element.
It's also worth noting that Jon has no desire to rule the Seven Kingdoms; he barely feels comfortable as King in the North. Since Dany's life goal is to sit upon the Iron Throne, this could prove problematic for their inevitable relationship.
The good: Jon is Daenerys's perfect match when you consider their life journeys. Each is alienated from a very early age, so they have experience feeling like outsiders even among their own families. Each stands up for the oppressed, with Daenerys freeing slaves whenever she encounters them and Jon working to save the Wildlings from impending doom even at the risk of his own position. (This is why he's killed by the Night's Watch — he stands up for what's right.)
Jon is the perfect foil to Daenerys: he is ice while she is fire. He is relatively cool-headed while she has a quick temper. He is cautious where she is quite often reckless. Together, the pair have the makings of a perfect couple. If they joined their armies, they would become unbeatable!
The sexual tension between the two is palpable, so much that it's almost hard to watch their chemistry without whispering "just make out already." Sure, they're not actually a couple yet, but we can predict the spark we'll see on screen when they finally give in to their attraction!
Finally, Jon gets along beautifully with Dany's badly behaved children dragons. What more could a single mom want?
