Just thinking about it now, but doesn't the idea that Rhaegar just decided to up and run with Lyanna because he wanted to hit that seems a little out of character? I mean this is the same dude who decided to live his whole life around being a knight because he read in some prophecy that he was supposed to be a warrior (remember, he was originally devoted to reading and music, he had no inherent love for fighting), the idea that he'd cast off his responsibility and throw the kingdom to hell just for some pussy seems a bit incongruent. And if he just wanted to bone Lyanna, he could have held a secret affair, instead of kidnapping her, which he would have had to know would result in their being chased down. But if he needed to make sure she conceived a son by him, and to be there to try have some control over the son's fate...
If we operate off the theory that Jon is his son via. Lyanna and that Jon is Prince that was Promised and/or Azor Ahai, then it seems more likely that Rhaegar found out that he/his first son Aegon weren't the one spoken of in the prophecy (as he originally believed), and since the Maesters had already told him that Elia couldn't bear more children, he decided that he had a duty to have another son, a duty which preceded his other duties to prophecy or to the kingdom.
Which raises the question of whether Lyanna specifically was required to bear the child (perhaps he came across another prophecy? Or had one of the 'dragon dreams') or whether he just chose whoever he'd rather do it with, although the latter also seems out of character, given how much trouble he caused from choosing Lyanna specifically. Perhaps the child for some reason needed to be of Stark descent? Born of Stark ice and Targaryen fire?
I dunno, I'm probably just repeating what others have pondered, but it just occured to me while reading the last page or so of the discussion here.
It also makes you wonder if the Maesters had any role to play in it. It's a bit of a stretch, but is it possible they manipulated him somehow, either with the content of the prophecy, or with Elia's health issues and inability to bear more children?
