SPOILER ALERT....
So it seems it's a safe bet now that they're going with the story of Jon Snow being a Rhaegar Targaryen's son?
I've only seen the show. I haven't read the books, but I hear the show is more or less caught up. If someone can't tell at this point who Jon's parents are, they simply haven't been paying attention to the show. THey drop elephant-sized hints constantly... especially this season.
IMO, he's the main character on the show and everything else is just secondary. Credit GRR Martin for the way he's crafted this story... it's full of misdirection, razzle dazzle and red herrings, but it's clear to me that the main arc of the story is Jon's. Every character we peak at in this world has some connection to Jon's arc. They serve a purpose in relation to Jon. You can't say that for any other character. If Daenarys dies, it doesn't at all impact the overall arc of the show. If Jon dies... well... that's a different story. It's like killing off Luke Skywalker in the second movie before he becomes a Jedi and having the third Star Wars movie end with Lando as the savior of the universe. There's certain conventions GRR Martin can ignore, but there's others that would just be weak storytelling. You can't make Jon's birth the entire reason we start peaking into the universe (why not earlier with the Mad King?) and then have it finish at an arbitrary point. Purely from a storytelling perspective, I see the only three ending options as follows:
#1 - Whitewalkers Kill everyone... that's a garbage ending
#2 - Someone random like littlefinger takes the throne... that's a hacky/arbitrary ending and arguably there's no reason at all to end it there. Ending it with littlefinger is akin to ending it with Tommen as king. What difference does it make?
#3 - Jon reaches his inevitable destiny. Wraps up the story arc cleanly. He has all the credentials: King's blood, the respect of the North, a moral upbringing, and years of service as Lord High commander earning his chops as a leader, and presumably... eventually dragons. That basically lays out every aspect of the show we have focused on. It all serves as providing more context for Jon's arc.
Just my opinion. I know some people think there will be happy ending involving Daenarys and Jon, but despite GRR Martin's penchant for flying fast and loose with the incest, I don't think we'll see Jon ending up with his Auntie. If she dies, she still serves an key part of Jon's story... as her main purpose is to provide context for Jon's true lineage... and introduce Dragons into the mix. Something tells me Dragons will gravitate towards Jon... and they will likely be a key part of the war against the White Walkers... what with Dragon glass and the process for making valaryian steel and all... If Jon doesn't eventually tame that big nasty black dragon and ride it into glory, I'll be a bit surprised.
Then again, there's also the possibility the crippled Stark avatars into some dragons at some point. Kid has to have some purpose, right?
I know GRR Martin has broken some conventions, but there's others you can't break. Not because "the man" forces us to think inside the box... because there are certain laws of storytelling that you have to adhere to. If you show a gun sitting on a nightstand, you at some point need to show the gun being used or it needs to serve a very important purpose in establishing something about your character. If you don't use the gun at some point nobody will say, "oh what a visionary... he added arbitrary random elements into his story"... they'll say, "that was hacky. Why did you waste my time by showing me the gun?". Everything in this story serve some purpose in context with Jon's arc.
Who knows, though. Great show.