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More pacing with actual stuff happening in between badges. I was loving X/Y when I realized I'd gone hours without my second badge, and didn't care, and was having fun in fact. I didn't care, since there seemed to be plenty to do and have fun with in between badge one and two. I wished the whole game had been spaced out like that.
Essentially, two journeys. You actually have the choice to either take on the league, or just kind of be an adventurer. Or even make contests your major focus.
On top of that, make contests a continuing thing, but updated. There's three rounds now: the round where the crowd cheers at you, then showing off your moves, then actually battling the other contestants anime style. Contest battles would have different mechanics than standard battles. Yes you're trying to take out the other guy still, but it's not your primary goal. You can actually choose more than one move, but there's certain limits that I can't think of right now. You can't just fuse all four of your moves without some sort of consequence though. You combine moves in an effort to make more appealing effects. Shit like ice aqua jet.
Multiple save files, or at least just a second save file.
If there were event mons, they'd have actual brief story event sort of things. Think something like a super condensed delta episode for every event pokemon. Or shit, a whole delta episode for an event pokemon.
Character customization is a thing in every game now. At least double the options available in X/Y too. And also, cross dressing is possible. If fucking animal crossing allows it I don't see why not pokemon.
Does /vp/ like my pokemon game?