I agree, overall a very well done issue. I was a senior in high school when 9/11 happened, and I actually bought this issue when it came out.
I also agree that it was a faux pas to have Dr Doom shed a tear. I understand the idea behind it ... the event is bigger than comics, it transcends the silly squabbles our beloved characters engage in ... but to me, the fact that it is so out of character makes the reader ask himself questions like "Is Doom more evil than Al Qaeda? Is Doom a hypocrite? Would Doom disapprove of 9/11?" This line of questioning feels crass, but is pretty much unavoidable. They could have avoided it by simply not having Doom in the comic, and for that reason, it seems like it's the one major misstep in the whole issue. Kingpin would have served their purposes much better, because it would be within his normal characterization for him to shed a tear in that situation. Presumably they wanted a more high-profile villain for the non-hardcore readers?