Hey, I don't know if this is still active but I just started playing through Nightmare Moon (trying to Nuzlocke incidentally), and I noticed a few issues:
-None of my Pokemon have been learning moves as they level up, for instance my Diglett should have tried to learn a total of three moves but hasn't tried to learn even one.
-TMs seem to be improperly randomized; I know the randomization of TMs wasn't mentioned in the OP but it seems like the flavor text for each move was randomized (Work Up for example has the text for King's Shield) but the TMs still teach the original move.
-Shops work perfectly fine for me, but I also was wondering if you had plans to randomize the inventory of second shops in locations that have them.
Thank you in advance for your attention to this! I posted this on GBA Temp as well since I wasn't sure of which was better to contact you on.