While I am more than likely in the whole "power-user" category (I for one didn't find PCGen to overly difficult to use, but that was many moons ago), I can completely understand and relate to where people are coming from.
It's not a matter of being unable to read documentation, or even to find it. It's a matter of being inundated with tech-speak from the get go, so users who are not tech-saavy feel overwhelmed, and move on.
If I started a topic about biology/biochemistry (especially using it in a game), there would be a lot of people that likely wouldn't even bother reading it, because it requires learning a lot of material just to read about it. That's leaving out talking about it or using it. I know it's a bit of an apples-to-oranges argument, but I think a similar thing happens with PCGen. The average chargen user, of whatever product, doesn't want to have to learn a new paradigm. They just want to create a character easier than by hand.
PCGen is a very powerful chargen, but from the get-go it's surrounded by parlance that intimidates the average role-player.
To pre-empt you kingpaul, what would I suggest? Well, I'm not a programmer, I'm a biochemist, so I'm in no way qualified to talk about GUI design, or programming.
Those aside, I would have a non-Sourceforge PCGen home page. Links on that page could link to stuff on SF, but Sourceforge itself is not built for users, it's built for designers. On that front page would need to be, at the very least, links to the documentation, to a FAQ, to the latest stable release, and to the latest beta (I would avoid alphas).
No, I'm not a web designer either, before you ask.
With regards to a FAQ, I'm sure on the PCGen forums and here you could have a call for questions, if some of the community members don't already have a good idea what is asked frequently. This is a good place to answer what may seem like simple things - just from this thread: "What is an alpha, and a beta?", "What is a release candidate?", "What do these numbers mean?" These are intuitive to people who have even a little experience with releasing software, but not to people who just download and play. I'd recommend breaking it up into a tree, one branch for each category of background info, installation, usage, customization (including coding data sets).
The other big thing I would do is link to tutorials on aforementioned page. I don't know if these exist or not - I haven't used PCGen since before 3.5. If not, I would recommend that the Code Monkeys
not write them. They're too intimately involved with the project, so what seems natural to them may not be for the average user.
I know these probably seem like a burden, when you're overworked and getting over the remnants of the whole Master Tools thing. However, you did say just a few posts up that you're not trying to limit users, and I think that these suggestions (and they're only that) might help with the less computer-saavy users.