>>58591423N has spent his entire life surrounded by abused Pokémon, he doesn’t know what the outside world is like, and precisely because he sees everyone happy outside, he wonders "how is this possible? I’ve seen all those Pokémon get hurt, is the outside world really like this? Or is it just a sham?" and to clarify this deep confusion he has, he asks you, the player, to face him with the legendary, because only someone more confident in their own ideas can win, but he wasn’t confident at all, precisely because he had seen all those happy trainers, he couldn’t explain it.
inb4 "why didn’t he just deduce that Ghetsis manipulated him?" because why would he have thought Ghetsis wanted to hurt him? From the outside it’s obvious, but he had no reason to think that, he considered him his father and believed he wanted what was best for him.