This idea looks good Varion! I have a few questions:
-Do Varion/Thorn have evolutions?
-Will the player have the choice between them?
-The battle vs the CEO will be a double battle?
-Could you say more about X Corp's plans?
I love the trains/bus/boats feature and the fact that some gym leaders do not focus on only one type of pokemons as well.
Good luck with this!