I agree with >>26 but I also agree that there's room for improvement.
Here's my take:

I agree that Requests/Feedback could use a little more exposure.
I think it would fit better under General, maybe later it can be put into
some sort of "Self-Moderation/Moderation" category.

Rules - 規則 should also be put more in the beginning. I dunno...

Team 4-ch F@H, 4-ch wiki, 2ch Portal and #4-ch@ZiRC could probably
be grouped together in a "4-ch Projects" category, also more at the top.

Two categories I don't really understand are "Lifestyle" & "News":
I think the only board that really fits under "News" is "News"... (ノ∀｀)
There's some threads in "Tech" that could be called news, but I dunno...
Maybe rename "News" into "General News" and create a new board
called "Tech News"? I wouldn't really know where to put "Politics", though.
I feel it doesn't really fit in "News"... "General" -> "General Discussion",
then put it there, maybe?

I think a better name for the "Lifestyle" category would be "Culture",
put "Net Culture" and "AA Bar" also in there and throw "Programming" out.
Maybe also put "Music" and "Film & TV" in there and rename "Entertainment"
(with "Anime", "Manga" & "Games" remaining) into "Hobbies" or "Otaku Hobbies"?

"Programming", "Tech" and "Science" somehow seem to go together,
but I wouldn't know a fitting category title. Maybe "Study"? 日本語 could
also be filed under "Study", perhaps.

Well, that's all from me. Have been enough words anyway, ne?