It's just scripting, although I didn't have to do anything explicitly for that- since Bill never takes you to the Sevii Isles, there's no way to finish the side-quest there, which is required to get the National Dex.
Ha Thanks! Just doing my bit to help the community. It'll be even better next update hopefully. Once I get to a point where I think it's pretty much finished, I'll eventually add improved graphics to make a full out more challenging Fire Red.
It doesn't work with YAPE. You can use PGE. I think PGE is better anyway actually, because YAPE ruins movesets.
The changelog for 1.2 is there to show what features I've added since 1.1a and what I plan to do but have not yet. It's not actually available for download because its not finished, it's just to show you what to expect so you don't change certain things. Ie. if I didn't warn of Johto pokemon getting new movesets, people might start doing things with the Johto Pokemon.