General (can be any topic that doesn't fit into the other categories)
Gallery/WIP's
Help (an isolated place to ask for assistance)
Feature requests (if u'd like. Could get crowded fast - such sub-forums always does :) )

That's only 4 and from the top of my head - but browsing would be much cleaner already and make more sense - as a MoI noob I'd be most interested in the gallery and help sections, and have already filtered out many irrelevant threads. A 100% clean forum can't be guaranteed but as long as ppl do their best to stick within the proper category, this forum will already be heading the right direction.

I understand there may be plugin support later? If that's the case then you might want a category for plugin developers. Perhaps one for development and one for releases.

Those 6 and 94% can very well have to do with the forum not being organized so ppl don't care about how they use the forum. Since it's all one big pile to begin with, it wouldn't make much sense in keeping each thread clean and that, I believe, can turn into a problem in itself - like reflecting as those 94%.

I didn't include announcements/news - if they are available from the site, then that's fine. I used the beta announcements as an example - but it's not the same with the gallery for the reasons I gave in my PM.

Edit: I almost forgot - don't wait till/after v3. You should do it now! :)