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As far as evil teams go, Team Rocket was great because true to their inspiration they had the same goal as almost every single mob or mafia out there. They sought to exploit the Pokemon world for money, often taking over buildings and areas and generally just being a bunch of wankers. They weren't nearly as unbelievable as the later evil teams, with the exception of Team Plasma in the first half of B/W. The fact that the player character even encounters them at all feels like complete chance, and the stakes are never so high that the fate of the world rests on your shoulders. No, if the player character wasn't there, the police could probably handle it. Just like in the real world. But the player is compelled to defeat Team Rocket because they are a bunch of no-good wankers.
Starting with RSE and continuing until now, the adventure started feeling much more like a tailored experience or a theme park ride. In GEN 1/2, your obstacles were all physical. I need to obtain this badge to show I'm capable of crossing the next route (because an adult is questioning whether I, a kid, can make it), I need to cut down this bush, I need to move this boulder, I need to cross this body of water. Now it's all story. You can't go there until you've seen everything here. You gotta do this or that because otherwise we can't move the plot along. Meet me at X location to move the plot forward. It all feels incredibly forced. This is not your world to explore, it's your world to experience in the order we deem correct.
I hope GameFreak's 2019 game which is meant for veterans of the franchise can recapture a bit of that earlier wonder. No more story focus, but rather a lore focus. Let the journey be both the challenge and the prize.