Much of it goes back to the Johto anime. Even with the target audience, it was a noticeable downgrade from Kanto/Orange. Not only was it overloaded with boring filler, but the quality of storytelling was lower than ever (GS Ball getting dropped, lack of real development for any of the main characters, Ash having a noticeably weaker team) and the tone of the series seemed even more childish than it was before.
Since so much of Pokémania was anime-driven, the anime Jumping the Shark spelled bad news for the franchise's popularity. People started losing interest in the series, which resulted in the Entei movie bombing in theaters and Crystal seeing a massive drop in sales compared to GS. GF hitting the Reset Button on the franchise with RS was the final nail in the coffin.
Ugh... Speaking of reboots. :rolleyes2:
If they wanted to retool the anime this drastically, I don't know why they're even bothering to continue with Ash as the main character. They should've just let him beat the Kalos League and finally achieve his goal of becoming a Pokémon Master and have his big finale as a character.