Canonically, I figure the strongest of the villains ought to be Cloud of Darkness. WHile several others have access to god forms (Kuja, Emperor Paramekia, Ex-Death for sure, possible Kefka and Jecht as well), isn’t CoD already a godlike being, just wrapped in a human shell? I never finished FF3, so I don’t know for sure.
If not her, then either Ultimecia or Sephiroth should get top billing. They’re both enormously powerful even without extra help. Ex-Death should be really strong as well, since he’s a 1000 year old super mage.
Kuja, Paramekia, and Golbez should all be on roughly the same level of power under normal conditions. Kuja and Paramekia should get power boosts in EX mode, but that’s not really considered “normal”.
Kefka, Jecht and Garland should be bottom tier. Kefka, of course, could probably go God mode with the power of the three statues, and Jecht probably has Braska’s Final Aeon form, but again, that’s not their “normal” state. And Garland should be low tier no matter what, as he’s just some schmoe in fancy armour.
So to summarize, FF villain tiers IMO:
Default State:
Top: Cloud of Darkness
High: Sephiroth, Ultimecia, Ex-Death
Mid: Kuja, Golbez, Paramekia
Low: Jecht, Kefka, Galrand
EX Mode inclusion (assuming various characters have God transformations):
Top: Kuja, Kefka, Ex-Death*
High: Paramekia, Cloud of Darkness, Ultimecia, Jecht
Mid: Sephiroth*, Golbez
Low: Garland
*I’m assuming that Ex-Death can take on some of Neo Ex-Death’s power. Likewise, I’m assuming that Sephiroth doesn’t become Seraph Sephiroth or does any kind of transformming. Obviously, this is all speculation until we get more info.