Regardless of how you saw Sansa's glance to Baelish, of all the women who triumphed in the finale (Pyrrhic victories though they may be) Sansa is the only one of them who not only gained nothing, but lost out on the title and recognition she felt herself due. She is without land, without title, and without an army. She has been through too much and knows that a woman in her position must have one if not all of these things in order to survive. The doubts about Jon were there before Littlefinger ever stepped on the scene- her mother openly despised Jon, and Sansa is a great deal like Cat. I don't think we can ignore the cast and creator interviews when they are stating the coming rift in such clear language. We can argue how effectively it was conveyed, but to me, it was crystal.
A Stark v. Stark plot makes sense from a story point of view- next season isn't going to be all white walker prep up North, that'll be for the final season. If it is about the fight for Sansa's soul or whatever, with Jon on the one shoulder and Petyr on the other, I think the more interesting and dramatic path would be for Sansa to listen to the devil. As for Littlefinger, the very act of telling Sansa about his vision of what brings him closer to the thrones is... part of the vision that brings him closer to the throne. If he was being candid with Sansa, or at least as candid as he can be, the goals of the Iron Throne and Sansa are intertwined. The show has tied those two characters together pretty inextricably at this point; that storyline isn't going anywhere.
What will be interesting is if Littlefinger knows more about Jon's parentage and if he uses that as leverage with Jon. He hints as much in the crypts with Sansa back in season five, though it's not really rocket science to put R+L=J together. I guess the aftermath of the war disrupted so much that no one really paid all that much attention to honorable Ned coming home with a bastard baby and his dead sister's bones. There were a couple of handmaidens in the room with her, one possibly being the book character of Wylla. Unless they bring in Howland Reed, there may be a chance one of these women talked.
As for Cersei, I can see her teaming up with Euron Greyjoy, once he realizes Dany and the fleet have taken off for Westeros. Fuck, what a crazy match that would be. Imagine a sea battle with krakens and dragons as Dany's fleet takes on Euron's. Euron looks to be the big bad before the final war. I don't think they are rethinking his storyline as they seemed to do with Dorne.
All the characters that get the most frequent death specualtion- Cersei, Littlefinger, Jaime- are players to the end.