I believe Nyx is pretty easily the best of the last minute Persona bosses narratively and visually, but I think that mostly has to do with the buildup, rather than the fight itself. Additionally, the boss probably made more impact for most back on the PS2 when it was actually hard, and not an embarrassing cakewalk where the supposed end all god melts like a little baby.
13 phases meant something when you were scraping by each one by the skin of your teeth, but it doesn't mean much when you can burn though 2 or 3 phases before your party turn has ended.