First; every town was in partial ruins with who knows how many people dead. If you didn't notice, Kefka wasn't concerned with outright killing everyone with his light of judgement. He already guarenteed that everyhing would die a slow death so long as he existed, and he was a man who liked to see people suffer. Also, magicite are what is created when Espers die. He finished off all but one that was still alive in the world after he killed General Leo (that one still being frozen in Narshe).
Second; Doma castle was the kingdom. There was never any indication that they controlled anything else, and there were no towns within a reasonable distance that we could even assume might have been under their control. Therefore, he poisoned an entire kingdom, and killed his own men in the process. It was a smart and ruthless thing to do, and far more sadistic than anything the other villians did. Also, you can't really assume that there aren't many people in the world based on what we see. Based on the number of people we see in just about any FF except XII, these towns must be full of nothing but inbred hicks as they certainly don't have enough people to support more than three or four families. The abilities of the consoles is limited, which limits how many people they can put in. Heck, there are more people in Midgar in Advent Children than in all of FFVII. What you see is just a poor representation of an actual world.
Finally; Meteor made people lose hope for what? A few days? Same with the void and largely the same with the others. Kefka became a god and ground the world under his boot heel for a year. Even if people could have stood up to him, they were living in a dying world. As far as anyone knew, there may have been absolutely no recovering from it. Even the heroes largely lost hope over the course of that year as they watched everything fall apart around them. No other villian has managed to plunge their world and their enemies into the hoplessness that Kefka did. That's why he's the best villian.






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