The show was set up to emulate the political environment of medieval Europe. Rhaegar's son would have been Aegon VI, like Henry VIII.
I mean, I get that the show and the books split, but I'm not thrilled that they merged Jon/Aegon. Of course, they merged Jorah and Jon Connington, so, hey, whatever.
But the symbolism that you need to remember is that Dany rides Drogon, and the remaining dragon is Rhaegal. Her three dragons were named after the men in her life that died (Drogo, Rhaegar, and Viserys). Viserys turned on her, and Viserion is the one the Night King is riding.
My guess is that Dany will ride Drogon, and Jon will ride Rhaegal.
I now seriously wonder how they're going to work Azor Ahai into this, but whatever. I think I know, but I'm not happy if that's how they choose to do it.