The story sounds very interesting, but it almost sounds as though it starts in the middle. I know you don't want to give out too many details, but maybe you should describe how you obtained your first pokemon or if you already have or something in that sense. Like I said, it sounds like a great story, I just don't think enough is explained.
Also, I'm not quite sure, but it sounds like each city will have a gym (arena is what you're calling it I guess) and it sounds like each one will have only one trainer to battle against. Maybe you could make each one have multiple trainers similar to the Battle Tower in the mainstream games. I could be wrong about your thought process, but this is also just a suggestion if you have not given any thought to something like this.