Since most FF villains fall into one of two categories, they aren't very broad. The FFT villains are exceptions however.

The reason Jecht isn't the main villain is because he isn't the one who has messed around with the party for the whole game. (Or, as noted, 'the final boss doesn't have to be the main villain'.) And yeah, big scaly monster. Seymour is the one that they tangled with for most of the game.

Same thing for Golbez. (SPOILER)Sure, Zemus may be the creepy moonman that was controlling him, but he's still the one they chase after, compete against for the crystals for a majority of the story. And can you say Deus ex Machina? :P

The others are pretty self-explanatory.

As for my favorite...well, I dunno. Kefka, who started the trend of type B villains, the Tactics villains for not falling into stereotypes, or Zande because of his wild hair. And the Emperor for me confusing Hilda's concept art with his, making me think he was a chick the whole time.