The biggest problem with the R=U theory is how many times Rinoa came close to death. If they were the same person, Ultimecia must be confident in some plot armor, or self assured in her continued existence regardless of how the timeline changes.

Then again, lots of movies stage these dramatic and emotional moments event if they make ZERO sense.
"We need her alive"
>forgot about the high speed car chase and shootout at the beginning.

Ellone was in Balamb Garden when Seifer launched missiles at it. Did Ultimecia need Ellone or not?