You have a lot going for your game that I really like. First off, after reading the plot, I see the potential for a full scale game which I don't see with a lot of other hacks. I love the screen shots! It seems like you really took the time and effort to create new places and add new features. The cloning machine in Professor Oak's lab is something to be excited about.
The dialogue is something worth noting too-one of the problems I've had with all the Pokemon games was that the dialogue was simple, and often pointless. With phrases like "..I'll avenge my friends and family," it shows that you put some thought into the character and what they would actually say in the given situation.
The only things I didn't really care for was the titlescreen. However, I think it would work a lot better if you just altered the color scheme to something darker.
Keep up the good work!