Game Of Thrones: 8 Ways Season 6 Spoilt The Winds Of Winter (And 3 It Didn't)
1. R+L=J Confirmation Via Bran
Like pretty much everything else in A Song of Ice and Fire, R+L=J started out rooted in the books, but was confirmed first by the TV series.
The theory that Rhaegar Targaryen and Lyanna Stark were the true parents of Jon Snow was(/is) the biggest in all of ASoIaF, with so many clues and hints pointing towards it - from "promise me, Ned" to blue winter roses - that it was basically more a plot point waiting to be confirmed.
Now it has been confirmed on the show thanks to Bran's visions, and we can expect it to play out in similar fashion in the books. Given that it's something that happens in the past, without any witnesses alive, then Bran's flashbacks are the only viable method right now for telling that particular story, even if it's just to do so to the readers rather than Jon. He's going to be having visions similar to the show - in fact, he's already started having them - so it makes sense that he would witness the events of the Tower of Joy, and the truth about Jon's parentage.
The only alternative to that is having Howland Reed turn up which, while it's a nice thought, doesn't look like happening anytime soon. The thing we don't know is how - and this goes for show and books - Jon will find out about his parents. Since Bran has been given the knowledge, it can be assumed they'll be reunited (especially since Stark reunions seem likely to increase) and he would tell him, though quite how you start that conversation I'm not sure. "So, er, about our father. Well..."
Now onto the storylines that Season 6 didn't spoil (at this point it should probably be pointed out that I've not included a few of these, because they're really different (Sansa, the Greyjoys), have been included in preview chapters (Euron), or are just completely non-existent on the show (Ageon).