In writing out my outlines for my Pokemon anime remix series, I kept the following rules in mind:
--Would this make sense in my own version of the Pokeworld, which is very different than the show we all know and love?
--Can I feasibly rewrite this into character development?
--Can I feasibly rewrite this into a step for the goals Misty and Brock (and other party members) want to achieve?
--Can this episode contribute to building the world, and expand on what we know and see from the games and the show?
--Can I take Team Rocket out, and still have some kind of a plot? (the answer I found in many of the episodes, not just in Johto, but the other game-based arcs, was "yes"
--Would the story suffer if this episode was taken out?
If the episode and its plot answered "no" to any of these questions (or "yes' to the Team Rocket question), it was either rewritten to suit my imagined Pokeworld, or removed entirely