When SciFi canceled Farscape for being too popular, the Internets told me it had to do with new leadership at the parent company that had some kind of personal problem with Farscape in particular and science fiction in general. This coincided with a sudden shift in focus at SciFi from, well, scifi to paranormal crap. I don't know how much of those rumors were true, but the paranormal crap all over SciFi was definitely crappy. It's become less prominent since then, thankfully.
Stargate SG-1 was the one show I liked on SciFi that seemed immune to its horrible tendency to cancel anything too successful, but I think I know why it finally succumbed. The show was fairly cheap to produce thanks to the plot device of the Stargate, but recently it had shifted to a more space opera feel, which required more special effects. Expensive effects were the biggest excuse used to kill Farscape. After all, the network can make a much larger return on investment spending ten dollars an episode to have plumbers videotape swirling dust clouds in the dark or by letting several people humiliate themselves by wearing pajamas and pretending to be superheroes. I guess the only reason Atlantis didn't suffer the same fate is that it has higher ratings at the moment. The ratings drop probably had a lot to do with MacGuyver leaving, along with other cast changes, which is unfair. Claudia Black is a great addition, and Ben Browder is starting to come into his own in spite of some rough spots as they tried to establish his character. I can understand why some people don't like the plot changes, but I'm enjoying the ride. Personally, I was getting bored with the show because it never seemed to move forward.