Incredible hack (especially one of the few actually implementing the right cries for pokemon expansions... :O) and currently rediscovering the battle frontier ! :D
Speaking off, though, here are some of the bugs I can report :
-> The move tutors in battle frontier don't teach the moves they list (Pain split in particular actually tries to teach "Trick")
-> The TM Poison Jab is not learnable by any pokemon even Mew
-> Trainers with U-turn, Volt Switch, and Parting Shot will make the game crash in the Battle hall, in Battle Frontier.
-> Pokemon with the abilities Pickpocket, and Magician are capable of stealing mega stones. If said pokemon are found in the wild and steals your item through abilities, KO'ing them will cause you to lose said item.
-> The power items don't give the Bonus 4 Iv's they are supposed to, only macho brace works.
-> Synchronize doesn't work when trying to get a specific nature out of stationary encounters
-> Not really a "Bug", but trying to use the cloning glitch made me realize that any kind of partial save, such as the ones done when mixing records (for those blissey bases) or trading will delete the "Items" or "TM" part of the bag, as well as giving you infinite of all Balls currently in your Balls pocket.
-> As a result of not needing incense for some breeding, some Pokemon are unable to inherit moves through said breeding, an exemple of which being Chansey only reproducing into Happiny even without the incense. Resulting in an impossibility to obtain an Aromatherapy Chansey, for exemple.
And here are some of my minor suggestions :D :
-> Training cave is an incredibly awesome touch which would be even more awesome if it branched off into 6 rooms with only one type of EV's per rooms
-> Training cave is super special awesome, but would have a chocolate cherry on top if the wailord sprite for HP's EVs had a Skitty sprite on the back (because HSOWA).
-> Reduce the level of wild pokemon fished in Dewford, because in a nuzlocke run, running into a level 34 Staryu with a level 20 team is game - ending :p
Anyway, thanks again for giving me something to do during these long train rides on my phone, and apologies for the long bug report - even on games I play for leisure I'm still a beta-tester at heart ^^'