>>52651368It's a really tough call between this and the Volo/Giratina fight
The professor/AI is a really interesting character but only really gets focus in the endgame aside from bits and pieces during Arven's storyline. Volo is with you from the start of the game, he's practically your rival and has his own complex motivation.
The professor wins out in terms of the setting and spectacle, the time machine's arena is a really cool environment and the whole framing of them dropping Master Balls down on you with crazy new Pokémon was incredible. Volo's team on the other hand is almost Cynthia's with a remix of her theme too, and that makes you shit your pants for a different reason. It doesn't get points for originality but it's a really strong call-back that sets the tone for the kind of fight you're in for.
Now the second part of the fight where the Legendary comes in is where they go in two very different directions. Fighting Koraidon/Miraidon is a victory lap, you get the conclusion of your own bike's arc in a very satisfying and cool way. It's dressed up very well, I imagine most people who have played other RPGs that do similar things could read the situation and follow what the game wanted you to do, but ultimately it is basically a scripted fight. When Volo brings in Giratina after you beat him it's a real 6v7 fight, and when you finally do take him down he just fucking gets back up with a sick guitar riff, and you realize you're fighting a boss with a second phase in a Pokémon game right before it tears you a new asshole with Shadow Force.
TL;DR I think the Volo fight wins out for throwing real curveballs at you and Arceus in general being so fresh and interesting after the last decade of mediocrity. The Area Zero sequence as a whole though was fantastic and absolutely raised the bar for what the mainline games should aspire to in the future. Pokémon games are JRPGs and it's about time they remembered that.