As much as I love this theory, it wouldn't make sense. D&D themselves said that the rest of the story was invented on their own and that they refrain from making spoilers, so it would be weird if Rhaegar WAS Jon's dad because the identity of his parents is one of the biggest mysteries, and I don't think that the writers would spoil it. It was semi-confirmed that Lyanna was the mom, since GRRM said that when they guessed the identity of the mother, they guessed correct, but I believe that in reality, Jon might actually be the son of Arthur Dayne and Lyanna. If any one wants to support this, say something.
