Gonna try and do this in Hard mode.
First, Introduce difficulty settings from the start for ALL future games.
>Easy is on par with Gen 6 games with their EXP All and shitty teams.
>Normal is on par-ish with Gen 4 games, EXP Share is a hold item, teams are larger and stronger.
>Master is Drayano tier, almost all boss fights have full teams with Smogon strats.
Secondly, I would bring back customization for good. Skin tones, haircuts, real clothing options for guys, the entire thing.
For my last trick I would rework IVs a bit. Rather than each stat having a max of 31 and all stats being able to reach that max, I would make it so every Pokemon has a total of 120 IV points, randomly distributed among it's stats. The Pokemon could still pass specific IVs through Power items and Destiny Knot. It would please Karenfags with their "All Pogeymanz are equal" silliness, but still make individual 'mons different enough to be able to run different sets.
>Example: a Pikachu with 20 in each stat might be a wild one you would find, a competitively bred one would have 31 in HP, Attack, and Speed, 13 in Defense, 13 in Sp. Defense, and 1 in Sp. Attack.
Last thing I would do because fuck the rules I'm Masuda would be take 10 points from Mega Chomps Sp. Defense to keep Mega Chomps speed at 102. I would also give it Sand Rush.