Except that it's completely different and I have no idea how you managed to compare the two. Sin is the main villain. Sure, it's controlled by someone from inside of it, etc., but it's Sin they wanted and needed to defeat - whether that's by kicking the monster's ass itself or by destroying the one controlling the monster doesn't change anything. Edea, however, was just the first boss. Following her defeat, the focus switched to Adel and Ultimecia.
You can't just compare the villains only because they're controlling/being controlled, when the circumstances are entirely different. If Edea was actually the final boss, albeit controlled by Ultimecia, then the comparison to Sin could be made.
Nah, Seymour is the main villain, Sin is a part of the world and the lore and a large part of the reason for why the story progresses the way it does, akin to Jenova in FFVII or Garland in FFIX. Edea is controlled by someone inside her, she's also the first real threat you meet but that doesn't make her the main villain does it? Being the final boss doesn't mean they're the main villain either. Necron was the final boss in FFIX but he was in no way the main villain of the game.