You should probably change Yu Yevon to Seymour, since it is almost the same as saying Necron as the villain of FF9 (at least that's what it sounds like to me).

Anyways, I have not beaten FF1, FF3, or FF12 yet, so I won't count the villains of those games.

The person to take over would most likely be The Emporer followed by X-Death. The Emporer shows that he is very skilled in leadership, since he ruled the world and used the Imperial Army to get what he wanted. (This does not mean he is a good leader though, just that he knows how to lead). Zemus is somewhat of an above average villain, but he doesn't show anything for leadership. X-Death had used The Void's sealed monsters to try and fight the heroes of FF5, so he seems to know something about leadership. Kefka also knows about leadership, but he's been known to things his own way, rather than the "normal" way. Sephiroth is basically a rogue as well, and he even killed his own group of "followers," so he wouldn't be my first choice. Ultimecia also managed to take control of Galbadia and Galbadia Garden, so she would also might be the leader. Kuja, again was also much like a rogue and did things his own way, so I doubt he would end up being leader.

They would all try to backstab, because they are all villains and they want more and more power. The most likely to succeed are Kefka, Sephiroth, and Kuja though; Kefka would be my choice because he waits patiently like he did with Gestahl, and you wouldn't have even suspected it. Kuja did nearly the same thing with Queen Brahne. Sephiroth is also my choice by the way he backstabbed President Shinra.