This is an update I thought might end up happening, and sure enough, it did. Things have changed for me and I no longer feel it's worthwhile to do with PokeGen what I had planned. That is, I no longer intend to charge for it.
As a result, I'm also no longer going to be updating the program. That's not saying that it's over. Mat has the source code for 3.1.10 and will be able to continue it. As far as I know, he plans on doing so. The source code will not be made public, don't ask.
I've reopened this thread, although I'm not sure what there is to say.