You're probably aware of it, but if you want to see one the best WWWThreads customizations, look at the new Gossamer-Threads support board:
http://www.gossamer-threads.com/perl/forum/It's simple, clean, easy on the eyes, etc.
As for features... adding in as many as possible to prevent as much hacking is great

Also, some thought to moving more of the HTML into template type files so that customizations were easier would be really neat. After functionality, design becomes very important. How easy it is to change the look of the Forum starts to become more and more important -- and with each new release, it means updating the code multiple times -- and lots of places for errors.
The shift to templates would be a radical redesign at this point, but what about putting the HTML into a code file that would be substituted at run time? Or, using an idea from "patch" make an HTML code file that could be changed, and then patched into the main code files. Doesn't have to be really elegant, and the patches could contain PERL code, too, since it would be a block-replace between marker tags.
Just a thought. It's an extension of "include" files.