BSG was great, my favourite show of the decade, but I think the rails started buckling at the end of the second season. The show's character changed palpably with the New Caprica thing. After that, and with every new development, the train wreck became more inevitable, though there were some great episodes along the way.
As for Seaquest, one of my overriding memories of that show was being scared poopless by the Ghost Ship episode.
Funny how this topic has become "How to ruin a good sci-fi show"
An attempt to make an on-topic point:
I think a good sci-fi show has to have a setting that is both fantastical, but familiar. The setting must be safe enough that we can come back to it each week and recognise it. So, a base or a ship of some kind. (The Enterprise, The SGC, Atlantis, Coruscant, etc, etc...)
If it doesn't have a nailed-down setting, it needs a cast of strong characters to keep the audience grounded. They don't have to be strong physically or emotionally, but their depictions must be strong - emotionally and morally consistent from week to week, with at least one character that the audience can really like. (Sliders is the only one I can think of that fits that bill, even Dr.Who has the TARDIS.)
It also needs that hook, the one story element, usually a bit of technology or a character, that makes it describable in a sentence - "The one with the Cylons", "The one with the Stargates", "The one with Spock", "The one with the talking dolphin". That helps spread it's popularity by making it more succinctly recommendable, and easily kept in the public consciosness.
Then again, two of the most famous Sci-Fi shows break these molds; The Outer Limits and The Twilight Zone.