Having Seifer as the final boss would have balanced out the end better - though seeing Seifer in drag attempting to acheive 'Time Kompression' would have been...somewhat odd.

On a more probable note, more background details for Ultimecia or a confirmation of the R = U theory, would have given me both a greater desire to actually beat Ultimecia, and a greater sense of satisfaction having done so.

Apart from that, I would suggest perhaps fixing a few minor plotholes, and giving a more substantial and believable leadup to the Matron/memory loss revelation.