If Pokemon had special abilities the whole time how come they haven't used them until Gen 3?
This applies for both the anime and the video games. What I'm concerned about is that Pokemon didn't start using their abilities until Gen 3. I'll give examples. In Yellow, your first rival battle was against Gary Oak and he had an Eevee, the same one
The developers keep changing the things to improve the games. It's not supposed to make sense because they never offered any logical explanation for their series.