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I would love to see a Ninja team. I'm not sure what they would be called, but ninjas are awesome. Their goal, however, would be implanting chips on certain Pokemon to become evil and work for them.
Don't judge me, it's the best I got lol.
Brilliant idea! HP regeneration would be unfair if you were catching a legendary at extremely low health or if you were simply knocking out the opponent's Pokemon.
I think the Pokedex is going great so far. And with the habitat list from B/W 2 it got even better. Although, I miss hearing the cries by pressing X like in HG/SS