Howland Reed + Ashara Dayne = Meera and Jojen
This is the quick and dirty version of the theory. To read the whole thing, which is about 6,000 words, please click on the spoiler tags below.
My theory is that Ashara Dayne is still alive, living in the Neck, and married to Howland Reed. I believe they met at Harrenhal, fell in love, and married. Meera was conceived almost immediately, and it was a pregnant Ashara who went back to Starfall or King’s Landing—perhaps forcibly sent there by her parents. After the Tower of Joy, Howland picked up Ashara from Starfall, along with their daughter, and went North. The story was put about that Ashara died, and she assumed the name Jyana Reed.
Once at Greywater Watch, the couple had Jojen as well, and have been living there ever since.
In sum, H+A=M & J
The evidence in brief is:
The Tourney at Harrenhal: Howland Reed is watching Ashara and actually makes a list of all the people that she dances with. This has no bearing on the rest of the KotLT story, and yet it is mentioned. Why? Meera, who is telling the story, would have no reason to mention this to Bran and yet she does. Why?
We are told by Barristan that Ashara had a daughter. If that daughter was not stillborn, and lived, Meera is one of the only candidates, due to being the right age and gender. She is about nine or ten months older than Jon, and therefore one of the only known characters born in the beginning of Robert's Rebellion.
Jojen got grey water fever, which is odd because while it affects the Ironborn, you would think that the crannogmen would be immune to it. His eyes are moss-green, which is a color given to mark seers. But what color were they before the fever?
Barristan Selmy, who loved Ashara, remarks that: "She wants fire, and Dorne sent her mud. You could make a poultice out of mud to cool a fever. You could plant seeds in mud and grow a crop to feed your children. Mud would nourish you, where fire would only consume you, but fools and children and young girls would choose fire every time." Considering how many things he has been wrong about so far, is he wrong about this too? Did Ashara choose an actual "mudman"?
We are told that Ned would have died at the TOJ but for Howland Reed. What does this mean? Was it crannog magic, or was Howland Arthur's brother-in-law?
Why was Ned so quick to defend Ashara if R+L=J? It would make sense if she was the wife of his bannerman.
There is specific language over and over again with regards to the Reeds and Bran. Towers, Stars, Falling, and Summer come up constantly. Hints for Starfall, Palestone Tower, and the Summer Sea, perhaps?
The Dornish are looked down on by the other kingsdoms, as are the crannogmen. The crannogmen are reviled for their guerrilla tactics, which are considered cowardly, something the Dornish also have in common with them. Howland has spent his life among the water, just as Ashara spent hers on the edges of the Summer Sea. House Reed also has an ongoing feud with House Frey, just as House Dayne has an ongoing feud with House Oakheart. Common ground for a romance?
This is really the theory in brief, and the rest of it can be seen in the spoiler tags with evidence and analysis.