Rather than calling it non-canon, it's best to say it take place in alternate continuity and even Wikipedia call it the same.
It's a retelling of the Kanto League saga, but with many changes, like Verity, Sorrel and Cross who replace Misty, Brock and Gary and many Pokemon appeared which were not there in original anime during Kato saga. Additionally, many story aspects were altered or newly introduced, while keeping a few same.
So it's a loose retelling of the Kanto saga taking place in alternate continuity. Now in same continuity, a second film is coming called Pokémon the Movie: Everyone's Story, which will be a pseudo remake of both the Orange Islands Arc of the series and Pokémon: The Movie 2000.