I would say 70 to 80% of each episode deviates from the source material, either through omission or fabrication (the Robb and Daenerys storylines, especially; Season One was more faithful). Some of this could be said to be "minor," but much of it sacrifices the authenticity of the story/world, and changes the characters quite significantly. In some cases, they seem to be writing themselves into a trap, if they still intend to go the same direction as the novels.
That said, I still enjoy the show, and forgive some of its transgressions, but others I have a hard time wrapping my head around.
While I agree that more episodes would be better, if they would change the layout it might improve the quality without upping the budget. Instead of attempting to develop every character every episode, why not focus on half of them, and alternate those groups? You could get more development in for each character each episode, and rid yourself of those 5 minute "scenes" where very little seems to happen. The last episode is a great example of what I'm talking about. Can you imagine it working any other way had they checked back in with Jon or Daenerys just to say "hey"?
Also, Book 3 will be split into Season 3 and Season 4, which is a great decision. It's definitely the most important to keep intact, and the most heartbreaking.