Along with Blakes 7, Babylon 5 and Farscape are my favourite TV SF series ever. There's no possible way to choose one over the other for me. Comparing them is equally impossible - they're so different there are no real bases for comparison. All you can legitimately say is that they're both SF shows. I will say that while no show ever made appeals to everyone, Farscape isn't for everyone - it's really like nothing else and can be too "out there" for a lot of people. If you get to the end of the first season and aren't completely hooked, it probably isn't for you.
Oh, and ignore references to "Muppets in space". It's an absolutely ludicrous comment / criticism, to put it as politely as possible.
As for the questions:
1. best characters - Farscape (just)
2. best storyline/plot - Babylon 5
3. best setting - tie. Both universes are fabulous.
4. best themes - Babylon 5
5. best acting - Farscape (just - IMO the acting in B5 is nowhere near as bad as a lot of people make it out to be, and Andreas Katsulas is - was - by far the best actor in either series)
6. best music - tie
7. best special effects - I don't care about SFX so no vote
8. best ending/finale - Babylon 5. "Sleeping in Light" is magnificent.
9. best overall - no vote. Along with B7, they rule.