Kämpfer/WMG

Natsuru undergoes a personality change like Akane when making the Kampfer transformation.
Honestly, at least in the anime there are times that Natsuru acts a bit too stereotypically feminine when in female form. Like worrying about people looking up her skirt while going up the stairs in episode 1. No one notices it because it's relatively subtle compared to the physical transformation.
 * It follows that whatever is making him act stereotypically feminine is the same thing that makes him Too Dumb to Live. Nobody could be that totally oblivious without outside influence. Given the other major behavioral change we see- homicidal ally-killing rage- its safe to say that the Moderators enjoy making the behavioral changes socially debilitating and funny to watch, so its a possibility.
 * Or the behavioral changes are designed to make the Kampfers in question more receptive to participating. Akane wasn't agressive enough to take part, so they give her agression. Natsuru lacks the feminine instincts to be undercover, so they give him those instincts- and remove enough IQ points that he doesn't notice the change, or think through the possibilities or implications of anything, like what he could do with a harem like that- something that if he did notice, he would pay far more attention to than to the competition. It didn't work, but you can see the reasoning.
 * The other justification is.

Sakura is a Moderator.
And she gave Natsuru the messenger deliberately. She liked Natsuru but she's gay, so she decided to solve the problem by making him a girl. The rest is just keeping up the Masquerade.

Natsuru grows a variant of the Tohno Gland when transformed.
It gives off pheromones, much like Shiki. It's different in that it not only attracts females, but also their forces their inner Fan Girl to spontaneously sprout and glomp her/be in a very close vicinity. No Sense of Personal Space close. Rape attempts are also an effect.

The story is a satire of the Magical Girl genre.
Think about it: the Evil Overlord (Shizuru, though it may change later) is just teasing the hero For the Evulz and succeeding to a degree instead of going overboard with world domination plots and failing. The love interests are all girls instead of feminine guys. The talking animal/stuffed doll companion is not cute, cuddly, or heart-warming at all. Don't forget the henshin sequence where not only Natsuru's body changes into a girl, but his school uniform inexplicably changes along with it.
 * Shizuru, who in a straight magical girl anime would easily be a villain character, is the most heroic of them all. She's the one who declares a truce and has the best motivations. She's also very aggressive, especially for a japanese girl. She's definitely a deconstruction of genre tropes.

Sakura is a Manchurian Agent controlled by the Moderators.
She is ordered to make the Messengers and give them to prospective KÃ¤mpfers. She carries out her orders subconsciously, unaware of what she's really doing. Also, she has a Weirdness Censor memory implant, which makes her unable to see the similarities between ♂Natsuru and ♀Natsuru, and unable to notice the KÃ¤mpfers' bracelet.

The White Kampfers weren't originally part of the plan.
The way I imagine it, the whole Red vs. Blue thing was set up for the personal amusement of the Moderators. But then Shizuku got involved, and negotiated a truce between the two sides so they could figure out what was behind it all. Cue the Moderators throwing popcorn at their TV screens and shouting "BOOOOO! This sucks! When are they going to fight?", necessitating the introduction of the White side.
 * This one is starting to mesh with 'Sakura is a Moderator' in likelihood. Since the tournament has gone off the rails; as lampshaded in the intro comment about the fight being forgotten; and Shizuku appears to be turning into a Chessmaster, Sakura has stopped playing nice. The only alternative explanation for Sakura's personality change is that there's a Sauberer with more subtle skills than launching fireballs (eg hypnotism, possession or mimicry,) but that's still too wild a guess at this time.

Akane is Blind Without'Em in Kampfer form.
As good an explanation for her (lack of) marksmanship as any. She just does this to avoid being presumed as weak during battle.
 * Think about the first time she attacked Natsuru in the anime, she stops because she sees the blue bracelet indicating they're on the same team. That's also the first time they were close enough that a nearsighted person would be able to see something that's otherwise fairly visible.

Dead Kampfers became Messengers.
Episode 8's eyecatch shows a girl with black bunny ears and the voice of Seppuku Kurousagi. Maybe the vanquished Kampfers didn't really disappear from the world but cursed into being CreepyDolls instead.

== Guess we can just come out and say it, Kaede is the secret Big Bad/moderator and has just kept Obfuscating Stupidity until her Evil Plan was complete(episode 9 is when it is completed and now she and the White Kampfers go on the move)and the real motive behind the Kampfers will be revealed now. == I'm guessing Ancient Conspiracy myself.
 * More like Red vs. Blue. IN SPACE! No kidding.

The three head members of the student council are Mods.
Because someone has to be, and we haven't seen them in a while...
 * Maybe we haven't and maybe we have. See any resemblance to the White Kampfers?

Sakura is a reality warper.
She once said that the Burnt Lion looks very similar to a drawing she once made. Maybe she subconsciously has some reality warping power, although not quite on Haruhi's level. Following that, all this happen because...
 * Ever wonder why their school is girls on one side, boys on the other? To the point of being walled apart? Sakura must exert some power on the environment.

Deep inside, she wants a great lesbian harem.

 * If the Kampfer form is someone fitting to her tastes, she will keep her. Otherwise, she will let them continue the fight and let them kill each other.
 * She gives Kanden Yamaneko to Shizuru for this intention, but Shizuru's too smart(and probably too heterosexual) to fall for that. She also gives Harakiri Tora to Natsuru in the hopes making him--who are already very in love with her--into a girl, which suits her taste better. Unfortunately, he starts to unintentionally forming his own harem which even includes Shizuku, much to her dismay.
 * The White Kampfer are recruited to fix this situation, and they seems VERY loyal to her.

Moderators(or whatever Sakura is) can use all three of Gewehr, Zauber and Schwert.
Not quite a mass guessing as this is actually implied in the anime. To be specific, the handgun is the Gewehr, the katana is the Schwert, and the hypnotism is the Zauber.

Natsuru is actually THE most well-informed character in the whole series.
It isn't that he's stupid. Far from it. In fact, he's the most fiendishly clever character in the show. Look at the situation the girls have put him in. He has three beautiful girls vying for his affection, all of which can transform into hotter and more powerful forms at will and each with their own unique weapon they could use to kick his tail with. If he chooses one of them, the other two could team up and kill him and the third girl. So what does he do? He launches a Xanatos Gambit to ignore all three and pretend to like Kaede. Because of this one of two things will happen: either a) the girls will fight it out amongst themselves and he'll get the victor, or b) the girls will decide on a Tenchi Solution and he'll get all of them. Either way, he wins.
 * This one has quite a bit of weight behind it, since Sakura states outright that Natsuru is in love with the three. And apparently that will cause the end of the war she's presiding over. Maybe because the babies of two Kampfers are super-powered? Who knows.
 * It's also very likely he knows about everyone crushing on female!him and reacts the way he does in female form cause he doesn't want to date people as a girl but as a guy. Shizuku is the only exception cause no one knows what's going on in that head of hers, let alone Natsuru (that and she likes his male form better).

This show is an alternate-universe Ranma 1/2

 * In both shows the protagonist is an ordinary guy who turns into a girl at the worst possible times. He meets a girl named Akane who alternates from shy and calm to rude and bitchy (Of course, they have a little Slap Slap Kiss). Natsuru/Ranma also manages to get an Unwanted Harem of guys and girls, even though he is still oblivious to other solutions. Several characters are either innocent characters to only seem innocent or animals who have human-like tendencies. Natsuru/Ranma doesn't even test out her body. Finally, both shows, although seeming like action with slight comedy at first glance, condescend into comedy with slight action. It makes too much sense.

Not all Kampfers are girls, just the ones Sakura chooses

 * It's never made quite clear what Sakura is, so it's not unreasonable to believe that she is not, in fact, a Moderator, but only some sort of Observer or other agent who's job is to deliver Messengers and thus choose and oversee the Kampfers in a certain area. Other Observers in other places (Germany?) have different methods of choosing their Kampfers, and different standards. Sakura only sticks to women because she is a Psycho Lesbian.
 * Burned Alive Lion explains in chapter 26 of the manga that the moderators have a matriarchal society, where women fight while the men stay at home. So all fighters have to be female.