I'm thinking that I will have custom built pokemon teams that you can pick from, and the team you pick will alter what your gym looks like. The Gym will be located in one of the last towns, but I'm not completely sure on names yet.
Well, if you think you can do it, then go for it. I am sure everyone would love to play such a game.
For the gym I think it would be cool if you could choose a few gym 'types', like rock, water, fire, and normal, and then create it like a secret base, and for each type of gym you pick, you would get different items to add to your gym.