I've been visiting desuchan since mid 2007 on and off-- I'm not quite a regular but I've been following the site and posting silently on occasion. While this thread may not be watched, I have noticed a few things that I'd like to share.
I think the most important thing to realize is that desuchan will never be as big as it once was back in its peak. There's not much that can be done about this; even S3 wouldn't bring it back to its old level-- unless someone wants to revive the practice of spamming desu everywhere, of course.
Boards need to be cut. Unless you are a behemoth like 4chan that will garner traffic irregardless of how many boards are in place, a *chan should not be overly saturated with boards, eg: iichan. The less boards there are, the more the traffic can be condensed; the more condensed the traffic is, the more active the boards appear to be. Having the illusion of "more traffic" compounded with having a more condensed list of boards attracts new posters and brings out lurkers. Just skimming through the list, I see many dead boards that have topics that could fit elsewhere: /peach/, /md/, /c/, /yan/, /pro/, /gar/, and /vic/ among others. It's nice and all that there is a /sandbox/ to try new board ideas, but it's important to trim what there is currently before adding anything else.
For the record, consolidating the maiden boards into a singular board is a horrible idea-- as said, they are part of the site's identity. On the same page, a Peach-Pit board isn't as much (unless you really want a Shugo Chara discussion that badly).
Get rid of "srs shit yoYou guys DO remember we have a /sandbox/?!?! RIGHT?????srs shit yo
Donate over9000 today!". Keep that type of stuff on the front page.
Update the front page news more frequently. It's not only shows that desuchan is active, but it also gives the regular users some affirmation that the site is still alive with progress.
Add a FAQs, and perhaps a short history (not that horrid one on ED). Desuchan has taken a few interesting twists and turns and has played the part as one of the bigger *chans. I believe it would benefit new users to have these.
...and that's all! It's been fun visiting this board on and off for the past few years, and I hope it stays alive.