Bear in mind your calculated vast majority doesn't include that beloved staple of Naruto fanfiction, either--the dreaded Main OC. Most of these are female, just like they are in HP fandom.
Anyway, it doesn't look like the girls are faring all that poorly, considering how vastly outnumbered they are by male characters. Sakura's got 209 pages of fic in which she's denoted as a major player, compared to Naruto's 268 and Everybody Loves Sasuke's 292. Jeez, even little Hanabi Hyuuga's got four pages.
But, hey, we're not actually determining what gender gets the most fic time here, anyway. Taking a glance at the first page of the section, the random stats appear to be:
9 - Fics starring one or more OC (2 of which feature GaaraxOC)
7 - Het fics (a variety of pairings)
4 - Genfics (no pairing)
4 - Yaoi/shounen-ai fics (all NaruSasu)
1 - "Naruto is raped by vicious older shinobi" fic

What's to be learned from this? OCs are all over the damn place. (And most people should be banned from writing rape fic, because they just can't pull it off.)
Certainly not every page follows this same template, but the fact is, you can't just assume that because 1043 pages of fic have no female character categorized as a lead, that they must ALL be yaoi. There are clearly more variables to be considered.
FF.net is perceived as a complete joke everywhere I hang out online (except for NarutoFan, which I've been stringently avoiding for my sanity's sake.) I believe it was some subset of the Harry Potter fandom that took to calling it "the Pit of Voles" once they mass-exodused to FictionAlley.
Frankly, I don't care much about the opinion of those who cry "FF.NET IS DROWNING IN YAOI!" as most of those people were against yaoi in the first place. Of course it's out to get them, that's how they perceive things. Likewise, I perceive the Hinatards are out to get me because I can't stand them and yet constantly run into them, so I try my hardest to antagonize them. :devil: Errr...that is...
The high-volume comms are still pretty unreliable (say, ones like fma_het, that are kind of a dumping ground for every pairing out there.) Whereas if I visit a comm specifically devoted to a crackpairing I like, I'm bound to at least find one or two things on the front page that I end up liking, or that at least are worth passing the time with. Eh, it's a crapshoot as always, but it beats FF.net by a long shot.
Yes, I imagine the difference would be that I specifically seek out yaoi fics and tend to stumble across most of the het ones. It sounds like you're the opposite?
Yeah, but who knows definitively how most of them would feel aside from Kishimoto and staff? We've never gotten particularly introspective looks at a lot of these characters. We don't even know for sure if Sakura still has a crush on Sasuke, or if Naruto's feelings toward Sakura have cooled. It's mostly guesswork as far as I'm concerned.
As for authors applying their own thought process to a character's personality to "bend" them...please, this is in no way exclusive to the domain of yaoi writers. A friend of mine is terrible at this, and she writes original fiction. Once upon a time, all her characters had pretty distinct personalities. Over time, they all began to resemble her more and more; they'd always react as she would to certain situations, say the same things, etc. It's bad writing, plain and simple.
It's far easier for me to swallow the concept of Sasuke/Naruto than, say, Naruto/Hinata. The latter requires an even more extreme bending of Naruto's character. Naruto barely notices Hinata's presence in the first place, so for him to plausibly fall in love with her takes a substantial effort on the writer's behalf; oh, yeah, and he still likes Sakura anyway, or we're pretty sure he does. At least Sasuke and Naruto have an established, fairly intense relationship, even if it is mostly antagonistic. (Classic fodder.)
I remember trying to write a yaoi fic sometime in high school (right after I got into it), and I had no idea where to begin, because of my severely limited concept of "how this boy/boy thing is supposed to work." I imagine a lot of the crappy yaoi authors have the same problem but go ahead and write it anyway, without bothering to, I don't know, research anything? Or they write it as they would a het fic, only with two males, so you tend to have a somewhat in-character seme and a totally emasculated and OOC uke. And then they employ the het-fic cliches, which are bad enough in actual het fics, but totally absurd in yaoi.
But again, a lot of people just can't pull off fanfic, period.
Kind of like how het fics beat certain plot devices to death (Canon Sues, "dear diary" fics, high school fics, rape-as-a-catalyst-for-romance, etc...my brain hurts just going there)? How about the Naruto-specific plot devices like "Sakura decides to fix up Naruto and Hinata because she honestly gives a kitten about Hinata--no, really?"
Fanfic writers beat everything to death. They've been doing it forever. The bloody Biblical Apocrypha are technically fanfic; it's not like we're new to this pastime. I don't see why the yaoi authors always have to be vilified as the Snidely Whiplashes of characterization when het and gen authors are equally guilty of their own rampant bastardization.
I'll agree with you on Jiraiya, though. Dammit, the man is straight. Nobody acts that horny just for the sake of appearing hetero.
LOL. Yes, by all means, I'd love to see this no doubt scientifically accurate study sponsored by Animerica. I'm guessing they polled their readership and the majority of respondents were male. I'd be willing to wager the readership of the publication itself is probably mostly male (as is probably the case with ALL anime-related periodicals, except Shoujo Beat, of course).
I've read primarily romance fics since I first stumbled across the very concept of fanfic in 1997. I assure you, that particular genre not only gets more action than any other, but it's female-dominated. By far. Unless most of the authors I've read/reviewed/chatted with in all these fandoms over the years were actually guys going by feminine pen names and claiming to be girls. (You never know, these days.

So...since I'm totally off the mark, why then, in your opinion or best guess, is yaoi such an overpowering force whereas yuri's sort of a blip on the radar in most fandoms?
You claim to not care for yaoi in the first place, so I'm not sure you understand the perspective of the "typical yaoi fangirl." (Because most of them are fangirls, indeed.) You can appreciate a yaoi fic on its technical merits, but you're not "in it (i.e., the fandom) for the yaoi."
I got into two fandoms (Saiyuki and Weiss Kreuz) BECAUSE of the yaoi potential. (Both of these series feature a main cast of four guys who spend most of their time together, often fighting with each other, and very few females are involved in either story.) I kept watching GetBackers because I thought Ban and Ginji's relationship was damned cute. I keep reading Tsubasa, even though the story keeps losing me, because I love watching Fai tease the hell out of Kurogane. Where there is antagonism between male characters, there is yaoi fodder. (Hello, SasuNaru.) Similarly, where there is bantering and teasing between male characters (rarer), there is yaoi fodder. Yaoi fangirls will see subtext EVERYWHERE (and more often than not, proclaim it as supertext.)
And then I go to the LJ comms and fic sites for recs. Bear in mind here I'm generally not looking for high art. I'm looking for something with proper, non-distracting spelling and grammar, some kind of enjoyable repartee between the characters, and...well...yeah. In most instances, I'm looking for the pr0n. Plot? What plot?
I'm not saying "every yaoi fangirl is like me," because it's totally not true, but A LOT of them are. Again, I've deduced this from fellow posters in the comms where I lurk, or even on more general-interest forums that have little to do with anime at all (where it becomes slash--House MD and Pirates are currently really popular in that area). When they ask around for fanfic recs, they're looking for PR0N. A lot of the anime fans like Naruto in particular because it's "so gay"--yes, someone actually said that.
One of my (girl) best friends doesn't like yaoi at all--doesn't get the appeal, finds it kind of distasteful because of the relatively conservative way she was raised. One time I tried explaining to her (in the cafeteria at IKEA, no less

Her eyebrows raised. "Oh," she said, nodding. "Yeah, I guess that makes sense."
(I should add that I'm not in Naruto for the yaoi. Believe it or not, I'm in it for the characters, because they really are engrossing little buggers and I want to see what happens to them. Sure, I love KakaIru, but it isn't even my favorite pairing--TsuJira is--and obviously I like NaruSaku, or I wouldn't be here.)
Conversely, I don't see guys getting into shoujo series (or whatever has appropriate subtext) for the yuri factor. I imagine they find the subject matter pretty boring. A lot of them seem to get into series like Haruhi Suzumiya because of the MOE factor--they find the girls cute or appealing, but it seems like they tend to go straight for the hentai titles when they're a-questing for pr0n. Plenty of hardcore yuri in that arena.
I think I'll quit there, since I can only have a "serious" fandom debate for so long until I start just cracking up over the absurdity of it all. It's fanfiction, for god's sake.
Something I neglected to touch on earlier:
If people like this actually exist, they're idiots. And:
Fixed.
