So you're saying we should keep the various sections? Even ones that no one has posted on in YEARS? Because let me tell you, as the guy who actually rallied to get the Super Robot Wars section made in the first place, I looked at it and found absolutely no reason to keep it separate from the Gaming section outside of "Waaah, but I am a fanboy, I want my favorite section to be a special little snowflake!". And that, unfortunately, isn't a valid reason. So I reluctantly let go, because it was for the best.
Those sections just clutter the main page up. When literally just one or two topics are still active, it becomes pointless to keep the whole section. It's like keeping Formula 1 grand prixes around if only Ferrari raced.
As for Negima and LH, they don't just 'seem' to share the same universe, they DO share the same universe. It makes sense to put them together.