I just started reading the books. I know I have horribly mangled the names but bear with me...
About the books and Ned + Lyanna and the Rhaegar business. Ned does not seem to hate the Targaryns the way Robert does. 1. Ned argued againsts Robert's plan to have Dany killed. He even quit being the Hand because he objected. 2. In the book when he is looking for Robert's bastards - Ned muses that Rhaegar was not the type to whore about. So - he does not seem to hate the man that for as far as the world knows kidanpped his sister. I think Rheagar had to marry Elia of Dorne for the kingdom but he loved Lyanna and she possibly loved him. Otherwise - why would Ned not hate the Targaryns the way Robert did?
Also, Ned remembers finding Lyanna in a room that smelled of blood and she was feverish. Dying from childbirth? He reflects on how what he promised her cost him. Was it that he claimed her child as his own to shield her from disgrace in death and to keep Robert from killing Ned's nephew because he is a Targaryn?
Jon may really turn out to be just Ned's, but I don't get that vibe from the books or even the TV show. There is a reason why we see so much of Jon (and I don't think it is solely to showcase the lands beyond the wall). And I noticed in the credits - Kit Arrington (Jon) gets noted singly while the other Stark children are lumped together. When an actor gets good billing that is always a sign. IMHO.
Sorry. Just had to get that out. On the board that post about the TV show, the other ladies have not read the books and I don't get a chance to just ramble.