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More fucking May.
That said, if there is any way you could have both Brendan/May and Wally appear all the way through the game? Gen 3's rivals were the worst.
Change Team Aqua/Magma so that they aren't total pushovers with a shitty purpose.
More obvious shit like
>Chill with the Tentacool/Wingull
>Change some of the music somehow
Make the legendberries obtainable before the Elite Four, specifically the Regi's. Also, after the 4th gym, make one of the Johto starters obtainable.
Add some character to the Champion. Put him in the storyline a little more. Have him show up in Petalburg City instead of Scott.
Last but not least, put some other kinds of Pokemon in Altering Cave. Something besides Zubat, but nothing so OP that you can run through the game with it.
Pic related, how to make a game more playable without changing the story too much.