Unironically the problems were with the franchise streamlining it's story, lore, post game, appealing to the anime fans, and sequel escalation.
>B-but nobody plays these games for the story you're just a lorefag!
That's why there's no soul left.
The 2D games had this metroid prime like feel of being able to piece together certain things the game didn't tell you and come up with your own theories, even back in Generation 1 like Blue's Raticate, Ditto possibly being a failed attempt at the Mewtwo project, and even meta stuff like theories on if the glitch pokemon were actually the remnants of the Johto pokemon that got scrapped because they turned into them when traded to Gold and Silver.
Then came the GBA and DS games with complicated legends and actual lore on stuff like the legendary pokemon, and there were honest to god events like the Azure Flute, Sinjoh Ruins, and Deoxys Isle and Darkrai that told bits and pieces of their own stories.
When Gen 5 came out, there was the God Stone, the ruined castle, and the original dragon.
Then Gen 6 came, and the sequel escalation came. Pokemon that had to be bred were given to you, the postgame was all but scrapped, Z was scrapped, and events were streamlined. Stuff like Eevee in Black 2 and White 2's park area felt like a gift, Gen 6's streamlining felt like they were trying to push people through the game as fast as possible, stuff like the legendaries in the Hoopa rings, Diancie just being given to you by some random guy, The Anistar Sundial being made of the same crystal of the ultimate weapon and never being explained, Zygarde never getting a sequel and just being given to you with almost no fanfare in Gen 7, and Eternal Flower Floette being in the code for years without being released. The story was streamlined, it didn't feel like a grand adventure anymore, it felt like details were just being given to you with again, no fanfare and you were being pushed to go through as fast as possible.