Thanks! I tried to follow Game Freak's mapping style as much as possible when making the new areas, so it's good to hear that they fit in! I might add trainers to more of the new areas later on, though I wanted some of them to feel abandoned or rarely explored, so that's why there are no trainers there.
That's exactly where I wanted the difficulty to be too! If you deliberately counter team the bosses they're easy, but that'll happen no matter how hard I make them, so it's better that they let you use any Pokémon you want to beat them.
I might add the Eon Flute and both bikes eventually, those'd be good QoL changes. Game Freak kinda did wild mon scaling with the wild area, but it would be cool to see a whole region scale that way too, even if it was only after becoming Champion. Regarding the crashes, did you download a pre-patched version by any chance? I'd like to find out what causes this and pre-patched ROMs are the main suspect at the moment.
Looks like a fun team! No Light Ball on Raichu though?
Illusion's a known issue, it's mentioned in the OP.