Honestly why lead with a rock-type gym leader? All it does is sway the player to choose a starter that has advantages over it, ultimately defeating the purpose of having starters to begin with. Black & White did something nice in the sense that the leader you face against depended on your starter, and the only disadvantage you had was that you would always face off against a type that was weak to it. It did encourage one thing, however, to actually train your pokemon and develop your team so that you could work against this disadvantage. Having a Rock type leader as a starter just kind of defeats that purpose.
I like some aspects of the story. There are many possibilities you can work with by playing with the whole Pokemon experiments idea. Maybe your fakemon could be mutant Pokemon, or humans who were transformed into Pokemon by genetic engineering. Just an idea to spice it up.
Aside from that, I just want to remind you that you don't necessarily need to conform to the games 100%. Why not have a different type combination other than the standard fire - water - grass? Why not make your rival less of a douche (even though it's amusing to have a rival you love to hate, i.e. Blue)? Why have elemental themed gym leaders at all? My only true criticism for this idea is that it doesn't really stand out. Keep in mind, you can go with what you want if you like, I'm just recommending that you play around with your ideas a little more.