First of all, there's no way we can determine who's stronger, we would actually need to pit them against each other, the only way to do that is Dissidia, not good enough though. While important, strength is the last thing I look in a villain, you can have a God like strength, but what for if you don't know how to use it. On the other hand intelligent villains proved to be more threatening, Kuja for instance, with few well chosen words and little bit of sorcery he threw an entire continent into chaos of war. If we're looking at brute strength than definitely Sephiroth even though I'm still not convinced, but if you want the entire package then Kuja and Ultimecia by all means.