Just finished watching it and came here to comment.
Excellent documentary indeed! Really cool hearing all those people who worked on it.
The deadly shadows part made me feel bad for him. It's a flawed game, for sure, not just because of constraints and technical difficulties, I think the wrong choices were made and only later they understood them. However, it's clear from the interview that it was obviously made with a lot of love and effort, and sometimes bad choices are not obvious at the time. And flawed as it may be, I still hold the opinion that the plot is at the same great level on all three games.
The way they worked at Looking Glass goes against all my instincts of any creative project. It was very much a chaotic group effort, there is no one person who you could say made Thief. To me that is a terrible way of making art, but I guess that it has its merits if it can produce Thief, system shock and deus ex.