I think a lot of the criticism the movie gets is because people misunderstand its selling quote:
A documentary that follows the journeys of indie game developers as they create games and release those works, and themselves, to the world.
I've lost track of how many people I've seen watch it thinking it was documentary howto on game development and then be offended because it really has nothing to do with game development outside of following the developers and getting their outlook on everything. That leads to another thing I see far too often, people wanting a detailed howto on making games thinking they will make the next huge game without any effort.
I personally liked the documentary, though watching the segments on Fish made his ultimate exit last year no surprise at all. The others clearly had a grasp on it, but still put everything they had into it. I'm glad it all worked out in the end (well guess it technically didn't for Fish).