My favorite plotholes:
1. Why has Ash never kept his promise to come back for Pidgeot? He clearly remembers he had caught it and mentioned it quite a few times since he left it. Ash even had an extended stay in Kanto but never even bothered to go back for it. I mean he went to Saffron City and Viridian City but not the forrest where his third Pokemon was left?
2. Why does Ash insist on using his Pokedex every time he sees a Pokemon including ones he's seen SEVERAL times? I mean he just used it a couple of weeks ago on a CHARMANDER at the Kanto Fair! He caught a CHARMANDER and raised it and yet he STILL needed the Dex to tell him that Charmander's tail is an indication of its life force?
3. Who is Viridian's new Gym Leader? Scott said that they weren't there yet and Agatha was just filling in.
4. What happened to Brock and Prof. Ivy?
5. What ever happened to Todd/Snap? He should have appeared at least ONE more time especially during the Hoenn/Kanto/Sinnoh Pokemon Contests as they would be ideal settings for great pics of Pokemon being flashy.
6. Why do Pokemon in the anime randomly use moves hat would be impossible for them to know? (e.g. Pikachu using Leer the one time)
7. Where did Hunter J come from originally? Is she from Sinnoh or somewhere else?