I received an email from David Ormerod of GoGameGuru today, which may be more relevant to the specifics of the time settings used in the AlphaGo vs. Lee Sedol match. He is a little busy with his baby at the moment, but indicated that it would be alright to quote him.
It appears that Younggil and David were concerned back in February that the members of the Korean camp weren't taking the match seriously enough, and might not be briefing Lee Sedol as well as they could. They contacted Lee Sedol's sister, Sena (she used to live in Sydney, incidentally), and requested that she pass on information about computer Go and to have Sedol consult with a computer expert. David indicated that Sena later explained the reasoning that Lee Sedol had in selecting the two hour time limit.
Here's a quote from David's email to me:
David wrote:Anyway, I don't think anyone has mentioned that longer time in a human vs computer match fatigues the human, but not the computer. This was a key factor in Lee's decision to choose 2 hours each instead of a longer time limit. He was worried that with both players using 3 hours or more he would get too tired and the computer would gain an advantage -- as you know, the match with Gu was 4 hours. He may have miscalculated this, but he thought he could play well enough with 2 hours and not get too tired.
So while it is possible that Lee Sedol miscalculated the optimal time settings for the match, it appears that he believes that
fatigue would affect the quality of his play, whereas it would not affect the computer. With a longer time setting, like with his match against Gu, presumably he felt that his game quality would be worse with the increased time.
Of course, this is not any sort of definitive proof as to the best time setting, but it at least provides some evidence for this theory:

If nothing else, I'd think that we can see that game quality is not so simple to analyze, just by looking at the time limits alone.