Clever and a gem in the works
I give this a 10 not for what it is right now, but what it will be.
Several suggestions that some may have suggested, but here they are.
A UI return button, though it is simple to just drag them off their little square I had a few issues at the Brock fight where they would not return. A little button that you drag them to would be excellent. The capturing system is interesting but could be a little more polished. Mostly as other people have said, once your pokemon get to a certain point, they might be overshooting the damage. There needs to be a bit of a tweak there to make it not easier, but a little more accessible.
The dialogue could be improved on, but it sticks to the dorkiness that was pokemon, so we can't really complain.
Aside from that, it has the potential to be great, though I say I am sorry it got suspended from the android marketplace, I am glad that you have come to newgrounds.
Best of luck in this masterpiece in progress.