I asked this question of our head Release Monkey. To summarize his answer:
It would be hard and nearly pointless
All code files are recompiled for every release. As such, they all would need to be included.
For the rest of the files (which make approximately 1/4 of the release), many are touched, and they would need to be included as well. Therefore, we are talking a patch that is no less than 75% the size of the full release, and probably larger than that.
These other files are primarily text files, which compress easier than the *.jar files (which are already compressed)
Due to PCGen's cross-platform nature, doing updates that work on every platform would be very dificult.