I just don't understand the idea that she "seems weird" or different in a manipulative way at the end. Seems like typical air-headed Aerith to me. She mentions sending up smoke and stuff. It might be bad writing but I don't think there's Jenova flags there. And the way it's directed, with a purposeful nod to the original art and her saying "goodbye?" Yeah, that's not an evil Aerith at all to me.
while you slept, the world changed