Well, GRRM does not plot out his novels beforehand. He has said he knows where the destination of a particular character or plot ends up; but the path it will take to get there is mostly unknown to him until he writes it.
I am sure he has many major waystations planned in his head and D&D took those that worked with their vision of the tale and ignored those that did not. That's the exact sort of thing that will lead to increased divergence in the path the show and the novels take to get to the same end point.
For example, I do not think that Bran ever leaves that cave again (in the flesh) within the books. His ability to communicate with others beyond the cave was carefully worked into GRRM's story by the inclusion of the Glass Candles, the (probable) requirement that you had to have at least MET the person you wanted to communicate with telpathically before in real life -- and the careful meeting between Sam Tarly and Bran at the Wall (and Sam never tells Jon about it). Then Sam is sent to the Citadel in Oldtown which is the location of one of the Glass Candles. And then there is Jaqen in the Citadel, too.
All of that is, I believe, the plot point which drives Sam's presence in the tale after he leaves the Wall. Sam is destined to be GRRM's magic telepathic relay between Bran and Jon -- and maybe the Armies of the South under Randyll Tarly. Except in Season 6, Sam on the TV series has nothing to do. The Glass Candles are cut out, the prophecies have no place or reason to decode them in the Great Library, and Bran has left the cave and is going to cross the Wall himself.
So where's Sam and what's he doing? Nothing and nobody cares. His importance has been written out of the story, essentially, and he is given things to do that aren't in the novels because the show downplays magic. Sam no longer has a reason to be in the show. Which is why he has had what, four scenes all season 6? Pathetic, really.
There are more examples of this, but that's the divergence between novels and show. They are wildly different at this point.