I feel like you think you have some sort of advanced understanding of ASOIAF from watching the show as many times as you must have but if you would read the book or even better let Roy Dotrice read it to you on Audible youll see that nothing could be further from the truth.

Why you would anticipate John and Dany having a relationship in the book is beyond me. Last I read John had 4 daggers in him and no maester to patch him up. Should he survive somehow, there's the little problem of his vow to the nights watch that I don't see him breaking having ed up winterfell to keep it. As it is in the book-- John Snow is dead. Now he might come back as a whyte unless Melisandre brings him back like Thoros did Lord Beric, which is plausible just not probable, he still ain't hooking up with Dany.