I still feel people get Aerith's relationship with Cloud completely wrong. I don't think it was romantic or flirting really at all. She sees his facade, and wants to tear it down. She doesn't love him because she doesn't know him. She sees that he's broken, that his mind is warped and shattered, and she tries to fix it. That's why she's constantly digging at his personal life, or trying to get him into a position where she can talk to him seriously and in private.

She know's something's up with him, from very early in the game. She's constantly questioning his thoughts and making him rethink his facade. And isn't she the voice that causes him to question himself at the inns and the other rest times?

She's an Ancient. She knows that something's wrong with Cloud, and she has an urge to fix it. She also has an instinctual knowledge of the Lifestream and the afterlife, so she knows her own love is waiting for her there, and she can still go meet him.