This is an idea I've been thinking of for a good while now. I would've posted about it months ago if it weren't for me getting side-tracked by other things and not really being able to find a good thread for it. In the end I'll post it here under this potential unpopular opinion header:
Mainline Pokemon, and by extension every single monster catcher franchise (Digimon, Dragon Quest Monsters, Monster Hunter Stories, etc.) is at an innate storytelling disadvantage compared to most other subgenres and mediums.
Now, why is this? Because simply put, the characters in Pokemon, no matter the quality of their writing, are not the endstate. I think this felt the hardest by villains especially.
This is the Egg Dragoon fight from Sonic Unleashed. It is one of Dr. Eggman's most badass moments in the franchise. As the fight continues you witness him getting more and more manic, commanding his latest and most potent combat machine to fire missiles and destroy Sonic at all costs while both combatants are hurtling towards the Earth's core.
You know why characters like Giovanni, Cyrus, Lysandre and Ghetsis have never had and can't have moments this raw? Because they are not really the focus. By the very nature of Pokemon, they are just backseats to their selection of creatures. And because of the themes of this franchise in regards to its creatures, the Pokemon can't be treated as mere extensions of them like a force user's lightsaber or a mad doctor's machinations. They are characters in their own right, characters who split away the focus from their wielders.
Just go to any comments section on a final boss music video and really pay attention to how the iconic human fights in this series are talked about. It's never "Cynthia beat my ass as a kid", it's always "Cynthia's Garchomp beat my ass as a kid". With a few exceptions like Lillie standing up to Lusamine you don't got huge human character-centered setpieces: Think Senator Armstrong tanking Raiden's barrage of punches with 0 effort, or the disorienting and chaotic antics of Dark Samus. Time and time again, it always comes down to "Hey, <Pokemon>, do the thing for me!"
I wouldn't be surprised if this is one of the motivations for the recent move to big asymmetric Pokemon boss fights. Totems, Nobles, Ultra Necrozma, Palkia and Dialga's Origin forms, they're all undiluted, untethered encounters that showcase personality through their battles like normal fights and are all the more memorable as a result. And hm, how interesting, what's one of the most acclaimed bits of SWSH storytelling? Oh yeah! The DLC side-story where a Pokemon goes through an arc! Ooooh on that note, how fascinating is it that in general the games most praised as the pinnacles of Pokemon storytelling are the Mystery Dungeon titles, which cut out the monster catcher problem entirely by having the things the series is named after be the protagonists, antagonists and everything in-between?
Now, this isn't to say good stories are impossible in this framework. They just gotta consider this issue and work around it. Ingo in PLA is a highlight because yeah you fight him, but you also spend time just hanging out and getting to know him. In this specific instance, in fact, his competency at Pokemon battling is in itself a character statement!