I think he had the end game in broad form (Jon is a Targaryen, Dany will bring her dragons to fight off the white walker menace, Arya is a badass) from the very beginning. You can see that from the beginning in those main characters. I just think that as he went along, writing what he felt like his characters would do as he imagined their motivations, he had no idea how to get the story arc onto the downward trajectory that would lead to the spot that he set up initially. He puts great stock in having internally believable characters, that each character is acting out of their internal thoughts and interests, rather than the needs of the storyline in general. It appears that those internally consistent characters that he's created is making it more difficult to get the story to end where he wants it to go, and to get the series to end in a good place. That's what he's been wrestling with in recent years, he's said as much on his Not-A-Blog.