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The "X would like to battle" text that appears when a battle starts should probably be changed to "You are challenged by X", seeing that the latter is what the games use since Gen 4.
Are any sort of changes to Water Sport and Mud Sport on the table? I was thinking that having them last 8 turns and reduce damage by 75% would let them be usable ever, instead of being learnset cruft even at very low levels.
Clear Body blocks Hammer Arm's speed drop in this hack, so that alone makes Agility sets better. (However, it has no effect on Strength/Curse for some reason, so if 2.0 makes that ability consistently block self-inflicted stat drops (which I really hope for) then that would make Metagross much...
Would it be possible to make the Pokedex show what egg moves the first stage of a given Pokemon can learn? Technically they are a part of later stages' learnset thanks to breedless egg move sharing.
Suggestion: have the game automatically ask the player whether they'd like to save after certain milestones (defeating a major trainer, catching a legendary and such). Pokemon not doing that feels ancient even for early 2000s standards.
If that really is the only issue you have then you can remove them yourself, or if you're lazy then make their mega stones unobtainable and delete those from trainer teams.
Not sure if you're willing to modify such aspects of the game, but any chance for 2.0 to include sound options? Just being able to mute music while leaving SFX and Pokemon cries enabled would go a long way.