Yes, I'm familiar with this theory and agree with your assessment of how it will play out. Seems like the likeliest and logical possibility given the breadcrumbs scattered for us, so far. I am not a book reader so am not especially familiar with Rhaegar (he's hardly mentioned in the show). Lyanna, we at least met briefly as a little girl, and as a monument in the crypt under Winterfell.
IA, especially re: the point about Bran figuring it out very soon (likely next epi/season finale). Jon will very likely not figure it out this season though. Personally, I know this is a BIG REVEAL for the show, but I don't really care all that much about this secret. Yay, Jon finds out he's not a bastard and has a legit claim to the throne!!! And...?
I don't think it invalidates the possibility of Jon and Dany hooking up. Auntie and Nephew. Weird? Nah. Them Targs swing that way. And back in those days, with nobility only wanting to marry one another, there really were limited choices for mates. Sooner or later, everyone is related to another in some way.
I care less about who gets to sit on the Iron Throne ultimately and am more intrigued by the Whitewalkers SL.
Given that Bran is a seer, his role in the future great big battle will be that of the sage. He will hold the key of how to destroy the Night's King. I think Jon will be the one to deliver the final blow, with a special, magic sword, to the Night's King, in the grand finale. Piercing his heart once again, and turning him back to his human form, right before he takes his last breath (as all men must die).
As for the great magical sword in the end, maybe its Jon's own sword, maybe his own welded with other key magic swords (Brienne's, Samwell Tarly's house swords), and a crazy idea I had, was the dragons melting the iron throne down, and the metals also mixing with the other 3 magic sword, to give a mother of a great sword....heh.
Then, they can look into Home & Garden magazine and find a comfy, cushy chair to use for the new throne. Maybe one with some nice floral patterns. Might make the new ruler more pleasing for his/her masses and less of a tyrant than the previous ones.