The reason not many great sci-fi comes to mind with specifically bad effects is (besides us, being sci-fi fans, more leinent and apprecative of older SFX work) it can torpedo a story, as I sort of observed. Bad acting and/or bad SFX, and indeed bad direction, can lower what might have been interesting into, er, something else.
Ah, now this you can quibble with. The first season in particular was very rough. It got better over time but never really equalled the contemporary Star Trek shows. One might praise the makeup designs (the Minbari were very well conceived, I think) but that's not the same thing.I never liked B5's sets much but its makeup was great!!