One common criticism I've encountered by those who didn't like the course the show took over the last 2 seasons is that the show became a lot more supernatural and a lot less science-fiction. More specifically, certain important events and motivations had a spiritual/supernatural cause rather than a technological or scientific cause.

While I personally loved the last 2 seasons of the show just as much as the first 2 seasons I can understand the criticism. The debate about how much of the supernatural element should be in science fiction is a major one that rages between fans all the time.

I enjoyed the characters.. they were real people with real issues that people have.