There are quite a few reasons the Negima section is comparitively dead.
There's what rag said about overall quality.
There's the fact that Negi is a badass genius harem lead. Fanfic writers therefore don't have a reason to write thinly vieled SI's because they're butthurt over a character being stronger/more popular inuniverse than him, like they do so often in Naruto fics.
Less... bad stuff happens. I don't mean bad as in plot hole bad, I mean bad as in character death and such. Therefore there is less need for fix fics. No one has permanantly died, bar in flashbacks.
Negima isn't incredibly popular. Such, its amazing, but if you compare it to Naruto, Ranma etc, its not that well known. There are two reasons for this off the top of my head. The first is the anime, which bombed. Without that picking up interest in the series, less people got into it. The other is the start, which was 2 and a half volumes of harem antics which can put people off and they dimiss it as a Love Hina clone.
It doesn't help that the fanservice never truly goes away.
Lack of male characters too. There's Negi, Kotaro and... that's it, until we meet Rakan.
That + the fanservice means a distinct lack of female readers. Not none, but less than you'd find for some of the more popular shounen series.
As a consequence of a smaller fandom, there are less people who find faults with it.
If more people read it, there would be more people who don't like the direction the series has taken. For example, many would moan about the lack of Konoka development. Just as many would maon about Konoka development at all.
Basically, the bigger the fanbase, the more diverse it is.
Length is a factor as well. As Rag mentioned, he's felt that the last 100 chapters were weak.
The longer the manga runs, the more likely it is that people will grow dissatisfied with it, either because they get older and mve out of the intended demographic, or because it takes a different turn than how they predicted.