I find Seymour: The Backstory more compelling than Seymour: The Character, if I have to be honest. I found the Baaj Temple bit fairly interesting, I wish they expanded more on it.
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Necron, he just comes out of nowhere
For mainline games, Barthandelus is easily the worst as he's not interesting and doesn't even really do anything until two-thirds into the plot. He just feels like "designated villain no. 130457" than something important to the plot. Seymour is my second choice for pretty much the reason Formahault mentioned.
In the EU of the franchise, Genesis or Illua. Laddy pretty much summed up my feelings about Genesis, and Illua is pretty much like Barty from XIII, largely feeling like she's in the plot because the game was contractually obligated to have a major villain despite feeling completely disconnected to the plot. She may even be worse than Barty since Barty at least has a goal and plan (though stupid at best) Illua doesn't even have that.
From your posts i see that worst doesnt mean most evil, but i shall include both meanings. The worst villain in terms of poor characterisation/gameplay has to be Zemus ("or should i say zeromus" which is quite an annoying line in itself). The guy doesnt even attack you he justs floats there forever until the orb is used on him, then he becomes impossibly hard. As for most evil, id say its hard to choose between kefka and sephiroth.
Necron, because he appeared only at the end when we know almost nothing about him.
I see necron as more of a clever plot device, an unexpected surprise
Hmm, I'd have to disagree. I mean, let's look at FFX quickly.
You have the personal villain: Seymour. I mean, yes, he isn't that great a villain and he's annoying as hell, but his function is to be the personal point of contention for Tidus and Yuna, primarily. Given how often Tidus goes "SEEEEEYMOURRRRRR!!!!" like, every encounter, he does it well.
You then have the impersonal villain: Yu Yevon. We'll ignore the inherent weirdness exhibited by that strange-as insect like state. But the main point is that he is considered an impersonal villain: he has no connection to any of the cast. He appears at the end, as ultimately the guy behind everything.
Now while you could say that Yu Yevon is like Necron, just appearing at the end to ruin your day, he's different in that he embodies the main villain of FFX: Yevon. Yu Yevon's existence is hinted at several points of the journey, and given how evil Yevon has been, it isn't a surprise that you'll be fighting Yu Yevon. The point is, Yu Yevon is clearly visible in the shadows.
Necron just pops up out of nowhere with little explanation. I'd consider that poor story-telling, to be honest, as opposed to being a clever plot device.
Necron embodies the concept of Death and is meant to serve as a final representation of the cast's struggles to live, as coping with life and death is the main theme of FFIX. So Necron works very well thematically, unlike Seymour who could be cut from the story and nothing would change.
That's kind of the thing about death, though - you never see it coming :p