It's not a done deal even if it is a good theory.
I'm sure before it's all said and done they'll probably play with that more to screw with people.
I'm leaning toward it's more likely to be the explanation to all of Neds weird recollections of a promise made to his sister just before she died and a message he wanted to send while in jail. He asked for a parchment and messenger bird but then changed his mind when Varys stated that he could not guarantee the confidentiality of any message.
And the stories that Jojen and Meera tell about a young Ned, along with his brothers and sister at a tourney before the rebellion.
However, given all that I don't think any of that means anything in regards to who finally sits on the Iron Throne if it actually still exists to be won by the end.
As we know Mr. Martin likes to upend tropes and it could be more effective to have a common fantasy plot line be true but then do something rather perverse and unexpected with it.
e2a
http://collider.com/game-of-thrones-season-3-4-george-r-r-martin-interview/
here is an interesting interview. George R.R. Martin recalls meeting the show producers David Benioff and Dan Weiss and how he asked them questions to make sure they actually paid attention while reading the books.
One of the questions he asked was "Who is Jon Snow's mother?"
If they had read it and accepted the on the surface answer they would have just said Wylla. As Ned says to Robert that's who he slept with during the war. However the producers recall giving Mr. Martin a more "shocking" answer to which George responded a smile to let them know that the shocking answer was the right one.
Of course R+L=J isn't the only theory about Jon's mother (and it might not be the answer the producers gave) but it is an intriguing theory about the answer to who Jon's mother is.
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