This is quite a good hack (of what I've played so far). Your maps are definitly a plus, but I really like the new pokemon sprites. I usually dislike them, but their level of quality is much higher than other new pokemon that I have seen. Good work.
@ Ezxen: I don't think they are glitches - they just havent been done yet (for example, Torchic is still a starter).
@ firefluffymew: The reason why you release a ? sign is cause you don't have a pokemon yet, but since you're in a battle, something has to be released.
So you've probably already realised this KoBRe LaiR, but at the beginning when you run up to save Prof. Kaity, you go into a patch of grass. And grass=pokemon. But if there is no pokemon then ... you die (more or less). Can you do something along the lines of removing the patch of grass?
Also, in Zyoforest, there's this - ht tp://img173.imageshack.us/img173/4237/treewalk1ry.png . (remove the space in http).
Good luck.