The Preferences window has been changed fairly recently to be better organized. If you have serious suggestions about how things can be changed to make it more usable, they won't be immediately dismissed (not that they would be immediately enacted, but they would likely at least be considered).
If the feedback is simply that all programs with lots of configurable options suck and are hopelessly bad, then the negative language especially accompanied by a lack of constructive feedback won't be taken well.
Sweet, I love when OSS is able to keep on chugging over the years. Gives me hope for the future in an otherwise very cynical world.
But I don't think that having a large number of options and preferences is an inherently intractable problem. I use many programs with lots of detailed preferences that are fine. Eclipse, particularly, I use all the time, and it's got automated systems and extensions and they all have tons of preferences and windows and views, and it provides a pretty good way of handling it all. I think that it might be the next closest program to Mafia in terms of trying to provide the user with a way to interact with something that doesn't have only one good way to interact with it; unlike, say, BitTorrent, which has many options, most of which you never use ever, and the average user interaction is that you watch the download meter just fill up without the program ever halting and asking you what to do next.
And I would love to have a complete back and forth discussion with you about that LostCalPolyDude, I think you're cool, but I think we can agree that this thread is not the place to have that out, because this thread is for Q and A about the "Make.meat.fast" script, and we should stay topical when possible. So, PMs or another thread or whatever if you want.