Flutter, Ramuh in this game is not actually strictly evil, hell he is a deeply pacifistic Primal in that he is in fact currently summoned and roaming the Sylphlands, yet he orders them not to attack, he will simply not suffer anyone hurting his children.

Nor is Titan actually an evil primal either, all he does is protect his children as well, his clash against Limsa is a simple matter of Limsa literally trying to take over kobold lands.

Yet, yes, their nature is terrible in itself. For them to exist they must consume aether, which is required for other things to live. They are, after all, born of chaos.

Their simple existance is dangerous, but they themselves are not always truly evil. Is that the end of the story?

(given that, I do personally like a Truly Evil antagonist, sometimes you just need someone that you can unmistakably murder and not feel bad about)