I remain convinced that George R.R. Martin never originally intended for Jon Snow to be a Targaryan.
There's all the reasons I've gone into before, but here's another that's just occurred to me --
If Jon isn't Ned Stark's actual kid -- why did he get a wolf?
The discovery of the abandoned wolf pups at the start of the first book is one of the first and most subtle, yet convincing, indications that there are supernatural powers in the world of ASOIAF, and they are deeply interested in the Stark kids. The fact that the wolf pups' mother was found dead in the snow with a shard of an antler from a gigantic stag in its throat can't really be seen as anything but an ominous warning from the Powers That Be as to the shit that House Baratheon was about to dump all over the Starks. And the wolf pups themselves -- one each, for each of Ned's true born kids, and then, off to the side, an albino pup, for the bastard kid named Snow -- again, this kinda shit doesn't happen by coincidence. It was Jon Snow himself who convinced Ned to let the kids adopt the pups, by pointing out that there were four pups to four kids... Jon's first notable act of selflessness, as he could only make that math work by omitting himself from the tally.
And then, of course, they find Ghost, off to the side, and he's obviously meant for Jon.
And none of this works if Jon is a fucking Targaryen.
Jon, like the Stark kids, is obviously a warg. He can slip into Ghost's skin, and the wildlings immediately recognize him as one. Where did the Stark kids get their warg blood from? Not from their idiot trout mother, that's for goddam sure. They got it from Ned Stark.
Yeah, I know, Jon's half Stark... his mother is Ned's sister, Lyanna. Maybe she had the warg gene. But 'here's four dire wolf pups for Ned's four kids and oh yeah, let's throw one in for that half Targaryen nephew he's calling his bastard, too, just to keep the suspense going' -- that doesn't work for me.
Jon Snow is Ned Stark's kid. Or he wouldn't get a wolf. Period. The end.
So who is Jon's mother?
Yeah. Good ol' Ned was schtupping his beloved kid sister. Or at least, he did it once, and she got knocked up, and the shame would have killed both of them, and ruined Jon's life worse than being a bastard would, so after she died in childbirth, Ned, suffused on every level of his being with guilt, just lied about it. Or rather, he didn't lie about it, he just refused to tell anyone who the mother was, and nobody suspected.
Why do I think this? A couple of reasons. First, when Tyrion Lannister first meets Jon Snow, he says "You have more of the North in you than your brothers or sisters". This doesn't have to mean anything, but it's the kind of line that an author puts in as a portent, or a hint, that he never means anyone to actually figure out. But how can Jon have more of the North in him than his noble born siblings? Simple. They're half Tully. He's all Stark.
Then there's this whole thing where Ned figures out that Cersei's kids aren't Robert's, but Jaime's instead. Now, every single other person in Westeros we've ever met absolutely loses their shit at the merest suggestion of incest, but does Ned? Nope. He's totally cool with it. He takes Cersei aside and says "Take your kids and head for the hills, honey, because Robert's gonna kill 'em when I tell him about them". A very strange bit of mercy and compassion from a guy who has every reason to be outraged at Cersei's betrayal of his best friend, and who is already furious with Jamie Lannister, too. And yet, he does it. Why?
Well, if he's been banging his own sister and had a kid with her, I'm thinking, maybe that has something to do with it. I can't think of anything else that would.
Now, I don't doubt that if WINDS OF WINTER ever comes out, yeah, Martin will tell us that Jon is actually a Targaryen, just like on the show, blah blah blah. But I don't think that was Martin's original intention. I think one of the big reasons Martin takes so long writing these books is that he can't stand it when anyone figures out one of his plot twists in advance. And he relentlessly ego searches on the Internet. So when he reads where someone figured out one of his cherished secrets, then he has to throw out whatever he's written and go back and write it all over again with a different plot twist. I think someone figured out the Jon Snow/incest twist, and Martin went "goddamit" and had to start all over again, and came up with the stupid ass Targaryen thing as an act of desperation.
Disregard the "you have more of the north in you" tip off if you want. That's just dialogue by some character who has no idea of the truth, so whatever. And Ned Stark's completely weird and utterly aberrant kindness towards Cersei after he finds out she's been betraying Robert with her twin brother... okay, maybe he's just a real sweetheart. (I mean, seriously? No. Ned's cool, but he ain't that cool.) But, fine, ignore that if you like.
But if Jon isn't Ned's kid, why did he get a wolf? Especially one obviously meant for someone named Snow? Who wouldn't actually be named 'Snow', if he were really the trueborn son of the last Targaryen Prince?
Jon Snow was never supposed to be a Targaryen. He was intended to be Ned's kid. That's what I believe. And you can disagree with me if you want, but that just means that like Jon Snow himself, you know nothing.