Board Thread:Questions and Answers/@comment-202.80.217.27-20160620145143/@comment-201.116.161.228-20160629001315

Eko is Oke... your entire argument for Jon not being a Targaryen is the lack of Targaryen features. But there have already been several non-incest Targaryens without Targaryen features. Plus, apart from Rhaegar, who else could be his father? He's definitely not an incest child of Stark and Stark. And unless Rhaegar allowed Lyanna to be raped by someone, which would be extremely out of character for him, the only possible father is him.

And Rhaegar was obsessed with the Prince who was promised prophecy, so him secretly marrying Lyanna isn't far fetched.