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This game look very promising, your fakemon and regional variant in particular look very interesting.
One point that immediately jump at me is about Schuckle and it's evolution, I don't like the fact that your forced the player to use it for the 8th gym.
I mean if I've played 3/4 of the game already, I've trained six pokemons that I really like and suddenly I must either dump one to put Schuckle in it's place or spent time training it to finish the 8th gym and then ditch it to take back my previous pokemon.
I admit it doesn't really appel to me.
You might give the player a choice, either they do the 1 on 1 fight with Schuckle or a normal match.