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Get rid of gym and the e4 or make them an optional sidequest
Introduce multiple dialogue choices in conversations
Get rid of the villain teams and just have one or two badguys.
Needs to be darker and take on more mature themes.
Introduce challenge mode roght off the bat. AI is greatly improved and uses competitive-style tacrocs, carryvmore pokemon, are higher leveled, have more variety, have every mon with a held item, and make it so you get less experience from each mon and less money. Also get rid of the EXP share.