In the anime, the main regions' Pokémon Leagues (Kanto, Johto, etc.) all have the same structure:

1. Acquire the eight regional Gym Badges
2. Travel to a stadium to compete in the regional League Conference
3. Win the Conference, and earn the right to challenge the Elite Four and Champion
4. Defeat the Elite Four and Champion, and become the new Champion.

The exception is Alola, which has never held a Pokémon League before and thus had no Elite Four/Champion. By winning its Conference, Ash therefore became the new Champion automatically.

The Orange League was a "filler arc", to stall for time until Pokémon Gold and Silver were released and they could begin adapting it. As such, it was much shorter:

1. Acquire the four regional Gym Badges (most of which are acquired through challenges other than Pokémon battles)
2. Beat the Supreme Gym Leader
3. Become a Champion, but not the Champion (so you don't become the new Supreme Gym Leader and have to face challengers like the other leagues; it's purely an honorary title).

The Orange Islands arc is canon, as far as I can tell. But because the Orange League is a) so much shorter, including omitting the Conference that was Ash's main stumbling block, and b) not in a region from the games, it's generally considered to not count.

In the anime, the main regions' Pokémon Leagues (Kanto, Johto, etc.) all have the same structure:

1. Acquire the eight regional Gym Badges
2. Travel to a stadium to compete in the regional League Conference
3. Win the Conference, and earn the right to challenge the Elite Four and Champion
4. Defeat the Elite Four and Champion, and become the new Champion.

The exception is Alola, which has never held a Pokémon League before and thus had no Elite Four/Champion. By winning its Conference, Ash therefore became the new Champion automatically.

The Orange League was a "filler arc", to stall for time until Pokémon Gold and Silver were released and they could begin adapting it. As such, it was much shorter:

1. Acquire the four regional Gym Badges (most of which are acquired through challenges other than Pokémon battles)
2. Beat the Supreme Gym Leader
3. Become a Champion, but not the Champion (so you don't become the new Supreme Gym Leader and have to face challengers like the other leagues; it's purely an honorary title).

The Orange Islands arc is canon, as far as I can tell. But because the Orange League is 

a) so much shorter, including omitting the Conference that was Ash's main stumbling block, and 

b) not in a region from the games, it's generally considered to not count.