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The way I see it, the fundamentals of the game don't need to be changed at all, because they're still strong and make for compelling gameplay.
The problem with the game is presentation. P.much all of the current flaws and issues come down to GameFreak/TPC either not bothering or not knowing how to present their game in a way that their fans actually enjoy. Consider just three points:
>It's so freaking slow
Everything from how the game starts you off to how it explains things to the flow of battles. It frustrates adult players who know how the game works and just want to get to the meat of the game, and it bores kids who have short attention spans. Everything needs to be snappier and more responsive; think about stuff like Fire Emblem and Persona 5, for example, where attacks resolve with lightning speed and you know the efficacy of your attacks by the way they impact their target. All the same information is communicated in a fraction of the time.
>They have almost no grasp on what makes people like their characters
GF has top tier character design oozing out of every single model in the game, but only a fraction of them are even remotely compelling as characters. Which is okay, I guess, since the game isn't like a social RPG like Persona, but even so GF puts a ton of work into designing Gym Leaders and Elite Four members who you fight one time, and then characters like your rival or allies are always generic AF, which saps your desire to engage with them.
>They aren't paying attention to how people are actually playing the game
I'm talking about things like difficulty hacks, self-imposed challenges and randomizers. These add a huge amount of replay-ability to a game where otherwise the only variation between runs is which Pokemon you use, which doesn't offer that much of diversity to the game experience. Something like the Semi-Randomized Regional Dex that's been posted around here for a few weeks, for example, would be a huge breath of fresh air.