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Game freak were encouraging us to use more pokemon in the game with the new mechanic and that's what I love in the gen 6 games. You could let the pokemon you just caught easily catch up to the team.
Maybe you should make the gyms slightly harder, I just played the whole game with only a chimchar and a whismur (now an infernape and exploud) and I defeated every gym with ease. If you make the gyms harder there will be more of a challenge. Maybe you could make the gyms harder and then balance...
When I browsed the internet I came across this beauty of a hack:
https://youtu.be/X_1m8p3BJaA
How did he make those 3d animations?
When I asked him that he sent me a link to this thread.