I think the R + L = J parentage is pretty much without contest - there's so much circumstantial evidence to directly support it and there is no other option offered.
The big question, really, is how this impacts the story. Howland Reed seems to be only the only person suggested who is still alive to know the truth of it, but even if revealed, what would it mean for Jon?
After all, the Maester he served as apprentice to in the NW was a Targ who could have been king but took the black - and that was no secret - so having a potential king in the NW is nothing new.
What it means in terms of how it may impact ploit is just plain convoluted - Jon can only be a legitimate heir if the previous Baratheon-Lannister dynasty is accepted as a usurption. Yet I can't imagine many people calling for the return of the Targs as rulers after the last couple they had were mad, bad, and dangerous to know.
I think the only thing it offers is a potential way to bring the kingdoms back into reconcillation - was it Dorne that had the twins the Mountain dealt with, and were seeking revenge for? In which case, Jon potentially offers a way to gain their respect through this. The Starks also held measurable respect.
However, I don't think Jon is being lined up for potential kingship - the way I've always read the characters, Sansa *will* be a queen one day. Question is who too, and I can't see that being Jon.
Additionally, Daenerys has always been set up to be a returning queen of vengeance who will bring fire to Westeros. Question is, will she be defeated, or will a truce be necessary.
This is where Jon perhaps comes in - if we find ourselves in a position where Sansa is queen of the realm and Dany is attacking it, this is where Jon - knowing his lineage - would be in a prime position to broker a truce. He would have the blood of both families, and his position by the Wall makes him entirely neutral.
Anyway ... think I've rambled beyond the subject matter enough for the moment.