I don't know if there is an issue with the fossils as I have not gotten that far yet (I'll let you know), but I have noticed some things that might be a bug (very minor though). On 4 point isle, I can't use the bike for some reason. Also, I don't know if there is supposed to be a map of the island, but the town map does not display 4 point isle (in fact, at one point it shows me to be out at sea). Other than that, I haven't found anything I recognize as a possible bug.
This is my first time playing a Pokemon game, and I'm thoroughly enjoying trying to catch em all. When I found mew, I didn't find it particularly obvious that if you defeated mew, you wouldn't be able to get mew later (I saved before, so it was fine). Some text somewhere would probably make that clearer, or maybe have rare Pokemon reappear elsewhere if you accidentally defeat them. Also, it was fairly easy to find mew, and I think having to work a bit more to get mew would make catching it all the more rewarding.
This is an amazing hack, and I'm having a blast. I can't wait to play your next one. You might consider varying up the main storyline a bit (if it's going to have the same main storyline as this one) to give some variation between games.