Hey! Erm... On this hack, you might want to think about Post Game. I get the storyline is going to be MASSIVE, but the thing is, after the game, you should think about adding things like Contest or Pokémon Refresh etc. If you kept on restarting the game OVER and OVER and OVER it would get really boring after a while. Maybe it could be decision affected? That would give a unique twist. Say for example:
Character (Lets say Prof.Oak)
Villans (Team Flare)
Oak: Will you take down Team Flare?
Yes would lead to a sub plot, whearas if you chose No, it would affect the reigon or something. Like the UB quest.
And maybe Character Customization? I know it would have no point as you cannot play online, but seeing the sprite change would be nice.
These may be big features, but these are my thoughts