Here's my theory: At one point, the game's story wasn't meant to be a stable time loop. It was supposed to involve the ability to change the future, or perhaps parallel timelines or some such. One Rinoa, dead in space. Another Rinoa, becoming the villain. Another Rinoa, our own, saved from either of these paths. But then, either because of time constraints, changes in scripts, or simply second-guessing their initial plans, the writers went back. Maybe they thought Ultimecia being Rinoa was too dark. Maybe it simply became incompatible with their decision to enforce a stable time loop: If Ultimecia is Rinoa from the future, then that means even knowing that, every single one of Rinoa's friends somehow failed to keep her from becoming the ultimate evil, because that is the mandate of a stable time loop: The future cannot be changed. Knowledge of it only leads to you accidentally reinforcing it.
And that'd be a pretty dick move to pull on them!