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I want gyms back, but I'd also like to keep totem battles. I think they would be nice "bosses" for wilderness areas or for places special to the plot.
Maybe the evil team boss wants to harness "totem energy" and at the end you have a fight with him where he uses a team of six totem pokemon Lusamine style.
It's the E4 I think should change. I'd like to see it function a bit more tournament-style (or at least appear like it). I'd also like to see it happen much, much later in the game. I'd love a Pokemon game that lasts long enough for the E4 to have level 80-90 pokemon.
