Btw, please make the puppets being used in the normal and hard mode versions equal to each other; you mentioned that some puppets will exclusively be present in the hard mode version of the game, but it would be nice to see the hacks being on par with each other, baring in mind that the hard mode version is just... well, harder, in terms of difficulty, but not puppet diversity.
Just a suggestion whatsoever.

Also, I had this random thought, not sure what you think about it, since it's your hack and stuff, but what would you think if marts are being revised to sell actually useful stuff and make the TM's that you can purchase in marts be placeable items scattered through the entire region?
For example, you could replace the TM slots at Celadon City Market with shards, assuming you intend to follow a similar concept like Touhoumon Purple.
If you happen to plan making an additional region like Aichi did (despite the... questionable quality of that region, let alone the route to get to it), placing the TM's from Celadon as placable items would make it easier and allow to not break things during main game (I guess some TM's might be a bit OP otherwise).
Then again, it wouldn't fulfill its purpose to be a
tweaked version and would be more like a hack on its own, instead of something that is meant to be an improvement.
But maybe, my suggestions deliver you food for thought nontheless, can't hurt telling what's on your mind after all, right?
I don't know, just random ideas.
Keep up the good work, will be looking for the next update. Hopefully, you are able to eliminate some of the aforementioned glitches, especially the Pokedex one.