hi warrior cat,
I played through this first release to Pewter and I found not some much bugs but parts that bothered me a little:
1. The title screen was still Fire Red
2. There are three Pokeballs
3. Oak makes it seem like there are different pokemon, so you should rescript that part
4. The Girl Assistant seems to be too near the bottom. I would suggest that you animate her a little.
5. It would be nice if you added a little more twist to the plot (introduce a gym leader early perhaps or have a Team Rocket appearance.)
6. You should place the berry onto the starter like many of the real pokemon games do.
there are some other areas that I might have forgotten but that is about it. Great start!