Agreed.

The problem I have with Rhaegar and Ashara is, I suppose from a literary standpoint, what would be the point, or end game here?
What plot device, or purpose would this new, and very complicated story line bring, as Rhaegar still has some explaining to do with Lyanna?

While I do think there will be a deconstruction of Rhaegars character, (especially the way Dany hero-worships him), and question the mysterious nature of Lyannas feelings in all this, I do by and large think he is a positive character.
And I think that R and A would take his character to truly unsympathetic.

Just a few things.

I noted that disussion said Ashara danced with several men, and Martin probably means for these individuals to be the possible suspects, but I also noted that discussion stated one of them was a Dragon, Rhaegar, but that was not correct. Rhaegar did not dance with Ashara.
They were:
A Griffin, (JonCon- not likely the Father).
A Red Snake, (Oberyn)
A white coat, (Possibly Elias Uncle who was a KG, but who also kept a paramour).
A Quiet Wolf, (Ned), but only on the request of Brandon, who she most likely became "acquainted" with.

Ashara was also a member of a Dornish House known for it's honor, and first and foremost, Bannermen to the Martels and owe them their loyalty.

Also, why wait until Harrenhal?
They were already a clique' at Court, so if Rhaegar wanted to engage in that, then he already would have, and most likely all the KG, including Selmy would have known, because there is no reason for Rhaegar to hide his affairs- the KG guard, not judge.
Aerys didn't hide his behavior.

I also tend to think Elia was already pregnant at the time of Harrenhal, perhaps in the early stages, but nonetheless, at that point, Rhaegar didn't know that this child would be his last.
(Though, I can see the possibility that Elia had miscarriages before, and their marriage was becoming strained under the pressure, but I think he would be more apt to set her aside than engage in the kind of subterfuge).
Also, the level of that kind of baby switching would need all kinds of privacy, and they had less privacy then than now, with all eyes on them, and probably many of them not friendly no matter how pleasant Elia was.
It would involve the Maester too which I doubt he'd give Elia Martel more loyalty than Rhaegar Targaryen.

I tend to think Rhaegar fell hard and fairly quick for Lyanna. The way Selmy says, "Prince Rhaegar loved his Lady Lyanna...." just the possessiveness of that statement suggests to me that perhaps it may have been obvious to many.

There is also an interesting scene in a Jon POV where he is thinking about his relationship with Ygritte, and wonders if his "Father" felt the same shame and ectasy, (paraphrasing), in his Mothers bed.
Of course he's thinking of Ned, but this could be a look back into what we'll see as some guilt on Rhaegars part for betraying his vows to Elia, though it was a political marriage and he made no claims to love Elia.

As to why Ashara might turn to a Stark,(Ned), his Brother Brandon would be the common denominator between the two, and while Ned might be resentful of perhaps Brandon and Ashara,(and there is a hint of what might be resentment in his statement to Cat about everything being meant for Brandon), he'd still remain the loyal Brother, but be sympathetic to Ashara.
If Rhaegar, or anyone else did this to her, Ashara would hardly confide in a man, and one she had just met.

So, I guess IMHO, the Rhaegar and Ashara theory is just too too much, with Lyanna thrown into that mix as well.
Now, if there WAS a Targaryen likely to dishonor Ashara, I'd put my money on Aerys.
That also might be a reason why Arthur Dayne, an honorable KG chose to engage in a speculated coup with Rhaegar, playing at politics, something KG aren't supposed to do as I don't think just being Rhaegars best friend is reason enough as R would be King one day in due time.

I tend towards Aegon being a Blackfyre given the signifigance of Bloodravens presence, and the emphasis on the Golden Company, or somehow descended from Aerion Brightflame and a female Blackfyre as that blood would be the only kind good enough for him to marry, even if it's illigitimate.
He did leave behind a legitimate son, who was passed over in the succession.
So, he's a dragon, just not Rhaegars, and given Varys sowing dissention between Rhaella, Rhaegar,(who were supposed to be good for the realm), and Aerys, I speculate he's working from within for the Blackfyre cause, and he can still think he's doing well for the realm if he believes the Blackfyres to be better.

http://www.westeros....Signing_Oregon/

Seems to me like there's no real genes to pass on as much as there is some reeeaaallllyyy basic genetics. More of a bloodline kind of thing, instead of alleles and dominant/recessive traits

For the record, I don't really think it was Rhaegar, it was just another idea I was floating. And at Harrenhal, I think Rhaegar was more busy playing politics to "fall in love" with Lyanna. Plus, I also don't think Rhaegar was in on a potential Ashara-Elia baby switch, I never said that.

But for interest sake, lets imagine this scenario. Elia was a political marriage for Rhaegar, he didn't love her, though he probably did like her. Elia was sick for a long time after the birth of each of her children. After she gave birth to Rhaenys, she was probably worried that Rhaegar was going to throw her over. To make matters worse, Tywin Lannister had his hot young daughter at court, both of them just waiting to swoop in on Rhaegar the minute Elia fell down dead. To keep Rhaegar from straying, Elia may have engaged the assistance of her friend Ashara. She may have asked Ashara to keep Rhaegar company, escort him to balls, go out riding with him, that sort of thing. And the agreement may or may not have extended to keeping Rhaegar entertained in the bedroom. From Elia's perspective, it would be better to have Rhaegar running around with a woman she trusts than to have him fall into the clutches of someone like Cersei Lannister. So I am thinking that there may have been an 'understanding' between Elia and Ashara and Rhaegar.

I don't think it disproves R+L=J. It seems like the Stark wargs of this generation were helped along "magically." That's why there are so many of them despite the almost literal impossibility. Something else is at work there and it's not just genetics. But even if it were, no reason why a brother and a sister couldn't both pass it on.