I agree with you on this. S6 was one of my favorite seasons, and I really liked what they did, but it became clear to me that GRRM didn't give that much informations to D&D as I expected.
If you look at Arya's storyline, in the first few episodes they used her chapters from ADWD where she is blind, then they used that one chapter that she has in TWOW as an inspiration to create that "Lady Crane plot" and then they concluded that storyline. I remember that one of GRRM's editors said that he could write a whole book of Arya's adventures in Braavos. And I realized that her storyline in Braavos is just a compilation of short stories without any plot relevance. When D&D finished her chapters from ADWD and TWOW, that storyline just ended and she returned to Westeros. I don't think that that development will happen that fast in TWOW.
And the Northern storyline in S6 is something that won't happen in TWOW in that way. I believe that Ramsay and Jon will clash, because there is foreshadowing for that in the books, and I really don't think that Stannis will be the one to defeat the Boltons, especially because we know from S6 that Jon will become KITN. I don't see how that can happen in an interesting way if Stannis wins. Maybe even GRRM doesn't know. LOL
So as I said, I believe that Jon will leave the NW, I believe that he will have a battle with Ramsay, and I believe that he will be the king, but everything else will be different in the books. Ramsay won't have Rickon, Jon can't have interactions with Sansa before the battle and that was the most important part of his storyline in S6. (I think that Sansa and LF will arrive to save the day in the books as well, because that is the only way in which GRRM can make the Vale storyline from the books relevant in any meaningful way for the overall plot),
And KL's plot is also a show original plot, from start to finish. D&D said that the Green trail was their idea. We can't be even sure that Cersei will take the Iron Throne in the books.
Tyrion and Varys won't be in Meereen ruling together in TWOW, and battle for Meereen will be something that will take place at the beginning of TWOW, not as a culmination of that storyline. And everything that Varys and Tyrion were doing in Meereen was in a way an adaptation of Dany's chapters from ADWD. They've cut other cities from Slaver's Bay in S5, and they saved that for S6. In the books Dany is dealing with problems inside and outside of the city at the same time, but in the show they've just dived that, and gave inside problems to Dany and outside problems to Tyrion. Selmy is alive in the books as well. I agree that tyrion will be Dany's Hand in the books.
Daario and Jorah won't be a part of Dany's storyline, and Jorah won't be trying to find a cure. I think that Dany will spend much mor etime with the Dothraki in TWOW.
Iron Islands and Riveralands plots are something adapted from AFFC. Walder Frey won't be killed in that way because Manderly used Frey pies in the books. They said that the Hound's storyline was show-original.
In Bran's storyline we got "Hold the door" from TWOW, but GRRM said that it will happen differently, and I think that everything else in that storyline was show original, including Benjen Stark as Coldhands.
Sam's storyline was show original, and his arrival to Oldtown was the end of his AFFC's storyline.
So when you look at S6 it really is just an adaptation of AFFC and ADWD in diffrent way combined with original material and very few spoilers from the books(Hold the door, Jon as KITN, Sansa and LF in the North, Tyrion as Dany's Hand and Dany's victory in Meereen and with the Dothraki, and I'm not even sure that Dany will be part of that victory in Meereen in the books).
And there is YG's plot in the books, Doran is alive, LSH is in the Riverlands, Brienne is not with Sansa, there are more Tyrells, you have that storyline in th Vale with Sansa, Myrcella, Stannnis and Shireen are still alive in the books. Theon and his sister are not with Dany, so they have different storylines in the North, Davos is not with Jon at all, he is searching for Rickon, and Tyrion didn't meet Dany in the books yet, Euron is much bigger character in the books, in the show it seems that he will be just Theon's antagonist, something that can't happen in the books, because they've never met.
So, yeah, I don't see how TWOW won't be a mess just like the last two books, I don't see how GRRM can finish this story in 7 books with this pace and I don't think that he will finish the books at all.