@RobbyBevard:
1. The giant main cast right off the bat. Even over 38 volumes Ken didn't get around to all of them, but initially it was really hard to tell who was going to be important or what quirks they might have…. and there were 40 characters right out the gate... and that only kept growing. Asuna was about the only one you could peg for a lead immediatley... but all the other girls and teachers and background characters... who knew?
True. As we've seen with the recent The Idolm@ster anime, it's hard to properly develop characters under a 22 minute time constraint when the cast is huge. The trade off becomes too much focus on a core set of leads, or less overall depth in favour of focus on each character. Ken got away with it by making Negima extremely long, allowing him time to focus on everyone…
...but I still don't see why Negima couldn't be a 200+ episode anime to allow for the time to develop all those characters. School Rumble had 52 over two series/four seasons, and much of the relationship building in SR was exceptionally gradual. There's a sister Kodansha series that ran in Magazine alongside Negima with a huge cast and no clear main or central leads until far later in the story. With an excellent, probably superior anime adaption to its counter-part manga.
The only possibility I could imagine is corporate meddling at the production level. Budget restrictions are often set by the companies investing into the product, and with some titles like School Rumble, the budget is sky high (for tons of episodes, at high quality) due to the money dumped in by the production group. Something I notice for Negima properties is no established publishing company put any money into it. Compare for Kodansha manga,
Cromartie High School - Kodansha, Production I.G, Starchild Records, TV Tokyo
Great Teacher Onizuka - SPE Visual, Studio Pierrot
School Rumble - Marvelous Entertainment, Media Factory, Sotsu Agency, Starchild Records, Studio Comet
Fairy Tale - A-1 Pictures, Dentsu Inc., Kodansha, TV Tokyo
Love Hina - Production I.G, TV Tokyo, Xebec, Yomiko Advertising, Inc.
…
Negima! - Kanto Magic Society, Xebec
Negima!? - Kanto Magic Society, SHAFT, TV Tokyo
Negima!? Natsu/Haru - Kanto Magic Society
If it's not obvious, Kanto Magic Society exclusively produce Negima related properties, and it's highly likely that's the corporate entity Ken Akamatsu is using to fund his own anime. Although I doubt it's merely him, the fact that we're not even seeing a TV channel involved with the first anime suggests nobody was interested in airing it when production began, so Ken (and friends?) would have had to personally put up collateral to get it started. Given Xebec probably had more at stake in the first anime than Ken, the changes and piss poor production were probably creative choices by them to make the anime more appealing to a TV channel (which ended up being otaku slot @ TV Tokyo). Although it's hard to praise Akamatsu for being openly disgusted at Xebec's changes when sponsors couldn't even be found to invest in the show, if he had a financial stake in it (which is more than any typical manga-ka has in an anime's production) it completely explains why he would be miffed. Xebec would have ignored or overruled anything he wanted out of the show.
Note KMS completely funded the OVAs, SHAFT wasn't even given a say in how they went, which might explain why they were the most faithful to the manga of all the animated works.
The question here is why Kodansha isn't investing in all of the TV spin-offs of manga it makes. Shueisha is involved with every one of its TV adaptions, which makes sense, because a good anime works as cross-promotion for the manga. This is why Kadokawa pumped the Haruhi anime with so much money, even though Kadokawa is a book publisher and otherwise has little to benefit directly from anime sales.
A possibility is anime rights might not default to the publisher, or possibly tankoban publishing rights aren't necessarily owned by Kodansha for a title that runs in Magazine. SR, for example, is listed as being published by Media Factory (a book publisher), meaning it's tankos came out of MF, but it definitely ran in Kodansha's WSM. Shueisha by contrast owns everything regarding a Jump property, and the trade-off for control and flexibility looks to be consistent financial support by Shueisha for spin-off products.
What I get from all of this is despite Negima's sales, it's receiving little support by people with deep pockets, especially Kodansha itself, which might be why it's not getting the super long + faithful anime treatment it deserves.
@RobbyBevard:
2. The split between harem comedy (again with a huge cast) and shonen combat series. Two very different genres that even the manga had difficulty juggling, and it did it pretty gradually.
Genre Shift is probably the major issue, although I think the nature of the genres was more important than the shift itself. Sure, we who've been with Negima since the beginning, and have adapted to the change. I seriously doubt otaku dropped Negima just because it became a shounen combat manga…it's still a fetish filled story and all the girls are "pure", which is a big deal with fictional heroine idols for otaku these days. But TV demographics and manga demographics are very different things, and I don't think Negima could have been slotted in a children's time-slot on TVTokyo with its initial premise. Time-slot change killed Code Geass and did substantial damage to OP for a while, so changing the slots after a time seems out of the question.
Gainax proved with Gurren-Lagann and Eva that it's possible to get away with turning a children's anime into an adult one, but the opposite is sort of like reversing entropy. Utterly impossible.