I don't see how this game has to follow the same formula as FR/LG.Guys, I do not think they will change the gym Pokémon at all. Have they done it in FR/LG? no, actually. At best they could do a "after national dex" Elite Four with some additions and 70-ish Pokémon
I mean, does Falkner really have to settle with a Level 9 Pidgeotto as his main Pokemon? At least give the man a Hoothoot!
I mean, their main Pokemon should be one of that Generation, so Bugsy should have a Heracross (Or Ariados or Yanma if Hera is too strong), Morty should get Misdreavous, and Chuck should get Hitmontop.