I think it would be fair to separate mods from total conversions. TBP like WoD and others would go under TC category for not requiring original FS2 to play.
However, that still wouldn't solve the Diaspora issue because you just replace one category with another. But you can't give each TC its own category either. If you want to keep things fair, then Diaspora would also go under TC category. Or if you want to give Diaspora special treatment, leave it to its own category.
Or, you can talk to Sandwich and design new forum index that utilizes screen estate better to display large number of categories and boards under them. The default index displays a lot of unnecessary information such as number of posts, topics and last posted. So get rid of those and make use of that space.
Traditional index page really isn't good for showing large number of categories and boards, amount of scrolling require is ridiculous. I only use "show unread posts since last visit" and it serves me well and I don't waste time going through each board one by one.
One possible design for index page could be that it only displays categories at first, then user selects category and it displays all boards under that category below the categories. That way you never get obstinate amount of boards thrown at you at once. To take it further, the index could allow to store last selected category to a cookie. So if someone only ever reads Diaspora boards, the category is saved for him/her and displayed when he/she visits the next time.
Be creative in how you do things and put that Sandwich to work.
But considering what pain the mainpage has been and still is. I probably shouldn't have mentioned this, as it'll never get done.