I think Pokemon grew into something so quickly that The Pokemon Company/Gamefreak had to act fast to capitalize upon it's success.
As the cost of technology decreased and had more capabilities, this was the perfect opportunity to continue growing Pokemon into the longstanding franchise that we all love today.
I think the old formula was starting to lose its charm. It was too predictable- protagonist vs antagonist, catch 'em all, beat 8 gyms and Elite 4, and thwart bad guys' evil plans... I feel like they've been taking risks in order to keep their franchise going strong. Of course people have issues with change... but if nothing ever changes than people will get bored eventually!
In my opinion, Pokmeon has stood the test of time by being able to capture the attention of newer generations of Poke-fans while not completely alienating the people who have been there from the beginning.