Put a Gym in Anvil Town! That part of the map can be fleshed out and make Anvil Town a complete city with it's own Gym.
There could be 10 Gym - ala the fighting type gym in Saffron City in R/B.
Also, parts of the map like Nuvema Town might not be accessable till the end of the game. Who knows? So, the Trio Gym might be a post-game triple battle.
The Shadow Triad would make really cool secret bosses. You round them up one by one across Unova, then you battle them together in a legendary dragon Rotation battle!
(the level 11 lilipup is the perfect cover for the shadow triad, or proff that the trio gym leaders are NOT that cool.)