The problem with Pokémon stories for me are how every single game represents the goal of "become a Pokémon Master" by defeating eight civil servants (or, as in Gen 7, eight wild animals) capped off with a gauntlet challenge of five extra ones at the end. It retains this structure even when later installments focus more on the evil team plots, sticking so steadfast to the fact that the Elite Four and Champion have to be the final challenge that you'll get the big epic climax involving literal Gods being awakened from their slumber by megalomaniac villains with the world at stake... and then after that's done you've still got a sporting event to finish before the credits roll. It's a complete and utter momentum killer each and every time for me. Black & White circumvented this most effectively - yes, you still have Gym Leaders and the Elite Four, but then the game wisely shunts the battle with Alder to the side for what really matters: the battle with Team Plasma. Ghetsis is still a much better final boss than ANY of the Champions and I remember being so disappointed when Black & White 2 fell back into old habits. Sun & Moon probably has the strongest core evil team plot, but once again it's marred by its climax not being the end of the story and instead you're forced to deal with the Elite Four and Champion battles at the end yet again. At the very least, making the Elite Four (Kahili aside) characters who already appeared in the main story makes it all feel a bit more personable, and the Champion being Kukui represents the player's growth better than every other Champion in the series. Getting to defeat your mentor actually feels momentous! Too bad USUM completely chucks that out of the window by making the final boss the dude you've already beaten countless times throughout the game already, completely undermining the achievement of becoming Champion.
But yeah, Pokémon stories would be much sounder if they just vetoed the whole league structure entirely, IMO. There's no reason that that has to be the only way to represent becoming a super strong trainer. It's a JRPG! Where you constantly level-up! Becoming super strong by the end of the game is an inherent part of the genre! Surely that gives ample room to create whatever story you want around that!!! Colosseum and XD: Gale of Darkness, while not part of the core series, still find room to have the traditional gameplay systems intact and not regurgitate the same Gym Leader plot for the umpteenth time in a row. Hell, the climax atop Realgam Tower at the end of Colosseum mirrors the gauntlet challenge of the main series' Elite Four/Champion battles while actually having stakes and consequence. Wish we could've gotten more like that in the main series.