With the Star Trek series being brought back from death and a recent article (with a lot of interesting comments to read) at i09 it could be a possibility. In the i09 article as well as the comments, there is a lot of possible reasons listed for the low success of Sci Fi TV shows.
After watching all of Battlestar Galactica, there seems like there are a few key ways for the genre as a whole to return to it's former glory. The major one problem is the quality of acting and writing. Unfortunately a lot of the mediocre science fiction shows are plagued with decent actors and un-original writing. New shows such as Stargate Universe are smart by getting a few big-named actors, that's what hurt Atlantis, but in the end quality actors all around matter more.
The way the stories are told also need overhauling. What BSG, LOST and other newer shows are doing is focusing on the characters and minimizing the sci-fi aspect. LOST is an incredibly popular show with a wide variety of fans and this season, we've been delving into time travel. Yet both shows are absolute sci-fi shows but they have fantastic acting, great writing and focus on characters, making the sci-fi aspects not as important.
It seems odd to say that, about a show like Battlestar Galactica when it took place on, essentially, an aircraft carrier in space with robots, angels and the like - yet it was the characters (+amazing acting) and stories that got it's big following. Yeah it had some of the best space shooting scenes, but it wasn't the focus and that's a big problem with todays shows. Related to that and the writing is realism and predictability.
People expect a certain bending of reality or exaggeration, with sci-fi shows, but there's also a limit. I always thought part of Stargate SG-1's success was some of that realism. Taking place in modern time with real places made you wonder if it could happen in real life. Now a sci-fi show doesn't have to be like that, but decently realistic sci-fi shows seem to be part of the future. At the same time, shows like Stargate Atlantis had annoying exaggerations. It seemed like the Atlantis team was invincible, they got out of tight spots every time - avoiding death so many times. There's only so many times someone or a group of people can have unlikely escapes from death, before it makes it predictable.
One of the themes in sci-fi shows also seems to be "darker". This has to partially do with realism and predictable plots, as a happier up-beat show where the "good guys" beat the odds a lot of times versus a darker sci-fi show where they have losses - it feels real. Comic book movies have already taken this turn (see - Batman: Dark Night) and with BSG and SGU, darker shows. (that's what's claimed for SGU, we'll find out later this year)
That about wraps it up. I just hope the upcoming Star Trek movie can get the genre it's "mojo" back, as the genre at it's peak can be so great to see.