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.
Babylon 5 is still one of my favorite TV shows, in spite of its dated effects. If the plot and/or the characters don't grab me, I won't be impressed by great FX for long.
Let's be clear on this - I love Babylon 5. I love it enough that I would stay up to 1am every Sunday to rewatch episodes I'd already seen on Channel 4 just because they were uncut at that hour. Unfortunately, today, the visual effects don't hold up, the sets look cheap and quite often it looks like Lennier's head bone isn't glued on properly. They did an absolutely outstanding job when you consider that they had no money and were producing a show that looked great for the time compared to shows with much larger budgets, but that's not why I watched it. I loved the story, I still do. In fact, I'm going to watch it through again soon. (I only just remembered this thread, sorry for not replying sooner)
Special effects can help tell the story, but ultimately it's the story that counts. For instance, Babylon 5 can't match the production values of Deep Space Nine or Voyager, but personally I enjoyed it more.