Okay, so I've been thinking, reading, and listening to what some of my compatriots have to say about Understanding. And while I'm not going to place McCloud up on a pedestal, I'm also not looking to write off everything he says either. I honestly doubt that it's possible to write a comprehensive theory relating to any media without being pretentious in one way or another. The very act of thinking about art in general terms like this assumes that the thinker can ultimately understand that art completely.
However, it's not the philosophy present in Understanding that ever captured my attention at all. It was the frank, solid examination of things like shape, color, and time in comics that kept me reading, and here, I was hard pressed to find any pretension. The conclusions might be different from what others might have come to, but all in all he's just talking about comics in a scholarly light.
Honestly, from what I've heard about the man and his encounters, it seems like McCloud is simply taking his own theory too seriously. While much of the point of Understanding was for the purpose of taking comics seriously, McCloud apparently has trouble with the idea that not everyone will agree with his theories and concepts wholeheartedly. It's kind of like a large-scale internet forum; there's some good ideas here, but it's too close to everyone's hearts for them to discuss it dispassionately.