So, I've encountered a bug. The girl with the level 24 Kirlia beat my team of all three bat Pokemon's first forms and then she walked up to me and the game froze I'm currently rank 1 as a Flying type gym leader. I don't know how much of that is significant but I'm giving as much info as I can...
I wish you had multiple save files. The process for trying to get more saved games is way too complex and when you have a game as versatile as this it really feels like it needs multiple saves.