I can see some of the resentments towards season 3. Let's look at the premise. The Xindi attack on Earth, was basically a way to look at the terrorist attacks on 9/11, and how vunerable and disassociated Earth was after the attack - the same feeling we all had after the attacks in New York that day. In essence, that is what Star Trek was about - looking at modern issues through the medium of a science fiction television show. Really, it was at the very heart of what the idea of what Star Trek was about!
The problem was people had begun turning away from Star Trek at this point. Voyager was ending, and the steam had already run out of that train...of course, people were giving up. Enterprise, which did have a great premise, like its counterparts, also got off to a sluggish, hit-and-miss start, but unlike the other series, the fans weren't ready to give it a shot like before, and ultimately failed because of low ratings. Something was needed to give the show the shot in the arm is needed, and because of 9/11, there was a storyline that people could relate to. Something real. Something tangible. Something that the audience could connect with.
How well was the subject handled? In my opinion, very well. I think there was a lot of forethought put into season three. We all knew what needed to happen - it was established in the end of season two. We all know how it ends, with Earth surviving. all that was left was to connect the two dots, and fill in the blanks. And, I think they did a pretty good job with the blank-filling. Okay, there were a few bumps in the road for me, such as "North Star" and "Hatchery" - and let's be honest, "Doctors Orders" was a spin off of Voyager's episode "One", although, I thought it was better written, and better acted than that Voyager episode.