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Make difficulty options that are picked (and locked in), at the start of the game. Difficulty would only effect battles, in the form of levels, trainer rosters, AI, and experience, it would not effect anything in overworld. Make an easy, regular, hard, and challenging settings, all 4 available from the beginning of the game. Obviously for each difficulty tier up you go, the better trainer rosters will be, including amount of Pokemon, levels, movepools, and items, and the better the AI will be (hard and challenging actually having some strategies). The higher difficulties also will use an experience system similar to Gen V's.
I think difficulty options are a no brainer. People that just want to play for the Pokemon and don't care that much about battles get their way, and those that want more challenge get their's. Make options in game also to skip tutorials when they appear, another no brainer. That's just the start of things though, other changes could also be made, but I think these are the first and foremost ones to be made.
