Why is FFVI considered the best? (SPOILER WARNING)

[Elpizo]

Kefka's character is puerile and dull. He lacks any motive other than that he simply craves destruction for no good reason. This is why people complain. Other Final Fantasy villians (some, not all) at least have some driving motivation behind their madness. Kuja is not a fair comparison to Kefka at all, as Kuja has the actual psychology of a villian. Kefka does not.

Zemus: I want that planet. KILL ALL!!!
Exdeath: I want the void! DEVOUR ALL!!!
Kefka: Life is an unworthy thing! DESTROY ALL!
Sephiroth: I am an experiment! I need to become a god! KILL ALL!
Ultimecia: I have no explanation! ALL EXISTANCE SHALL BE DENIED, FWAHAHAHAHAA!!!
Kuja: Why would live deserve to exist without me? KILL ALL!!!
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Garland: I will knock you all down! HAHA!
Emperor: POWER! UNLIMITED, POWEEEEEEEEEEEEEERRRRR!!!
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Xande: Wait a second??? I get mortality? WTF, Noah?! No way I'll agree with this!!! Let's stop time so I won't die!
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Vayne: He's no badguy, just a guy with different views.
And I don't know about Seymore, but I think he's in the list of kill-all villains as well.

Yeah, really, FF is full of well developped villains with great motives.
Kefka's twisted mind convinced him that life was an unworthy thing, and that drove him to destroy all. That's as good as any other insane badguy. And FF had a lot of those.