Sekirei/WMG

Akitsu is/was Sekirei 07.

 * Akitsu is quite powerful, able to hold her own against Homura (Sekirei 06). She's got elemental powers, which are overwhelmingly clustered towards low-numbered Sekirei so far (03, 06, 08, 09, and 11/12 have them. Possibly 05 as well. The only other ones we know of are 107 and 108). And so far, Sekirei 07 remains conspicuously missing.
 * As a bonus, since iirc she lacks an Ashikabi, there's a distinct possibility Minato will wing her eventually.
 * It is impossible for her to be winged, and she does have an Ashikabi(The south, btw), still, she is with him entirely by choice and may pull a Heel Face Turn.
 * Akitsu choose to act for the south because he accepted her problems. She also isn't officially in the game, because she has never been winged and Minaka announced that all Sekirei have been winged. And remember, Minato is very special in the terms of the game as an Ashikabi. May be like Seo in that regard as well.

Minato and Yukari's father is Minaka and/or Takehito

 * Pretty straightforward. Minato's mother worked with them (and still works for Minaka), so either (or both) could be the father of her children. iirc, Minato's been implied to resemble both of them (Minaka by Kazehana, Takehito by Miya). The fact that the identity of Minato's father is apparently classified information seems to support this.
 * Pretty much confirmed to be Minaka.

At least some of the information Miya's withholding directly involves Minato somehow

 * Miya and Matsu clearly know much, much more than the former has currently allowed to latter to reveal, and it seems certain Minato is directly involved with at least some of it. Seo Kaoru, too, knows quite a bit Miya won't let him tell (and the fact that he's got some sort of Anti Magic just raises more questions)

Minaka killed Takehito

 * Miya's reaction to being asked what she'd have done if Homura had told her about their goal of killing Minaka pretty much says it all. Minaka did something to cause Miya to have that reaction, and the fact that her husband is dead seems to suggest the obvious.
 * Pretty sure that if Miya believed Minaka to be responsible, she wouldn't need anymore reason than that. However, Minaka is probably idirectly responsible, i.e. he could have taken action to save him, but for whatever reason, chose not to.

Higa kidnapped Yukari as some sort of gambit against MBI

 * Really, he's got to know she's the daughter of Minaka's Dragon, so the only reason he'd be doing something this outright stupid is if he's got something planned. Presumably his attempt to ally with Minato (where he actually asked for Minato's help in resisting MBI, giving some credence to this) was made for the same reasons.
 * It may also be that he wants Minato on his side, and if he doesn't join willingly, he has a hostage. Shiina is strong, but Minato has some of the strongest Sekirei out there.

Musubi is Karasuba's Morality Pet, and the only thing keeping her out of Complete Monster territory (and even then, barely)

 * She's the only person we've actually seen Karasuba be nice to. iirc, the best we get with anyone other than Musubi is Karasuba being civil to Miya (who iirc was none too pleased to see her), and that was probably only because Miya is stronger.
 * All but confirmed in the manga at this point, apparently the only reason Karasuba hasn't gone on an unstoppable rampage to nix all humans due to a bet with Yume over who would win the Plan. Since Musubi is something like the reincarnation of Yume, Karasuba is waiting until they're the last two Sekirei remaining before killing every human being (probably finishing with her Ashikabi, or perhaps using her wish from winning the tournament to do it all in one go)

Minato was experimented on as a child, and just doesn't remember

 * He caused 6 Sekirei to react with him, 4 of whom are Single numbers, and one of which contains the soul of a single number. His mother is an MBI scientist, and it is hinted his father is too, (Minaka or Takehito, take your pick), he is 19 at the start, meaning that he would have been concieved some time after the ship was found. Conected to a previous WMG, something is being kept from him about himself, possibly this. Also, as Seo has demonstrated, Takehito at least has no problems doing human experimentation.
 * He is the only one who it has been confirmed to cause a reaction with multiple Sekirei, the others with more than one are shown to take extras by force.
 * Possibly he is part Sekirei, part human.
 * There were 99 unfertilized eggs on the ship. Who are the fathers? Perhaps the reason why Minato is a strong Ashikabi is because Minaka contributed himself to the S-Plan (probably not only him due to the variety of Sekirei). Some Sekirei might be his half-sisters!
 * Weren't those eggs fertilised?

The ship that brought the Sekirei to Earth was a seeding ship

 * Its purpose was to seed the planet with Sekirei. Most likely it was one of several. Something went wrong on route, causing it to crash land. This may explain the male to female ratio. There is only so much space available, and having more women than men would allow for more births in a shorter amount of time. Because the ship crashed, Miya wasn't woken to begin the process. It wasn't until Minaka boarded that the ship began to awaken.

Minato will be the Big Bad for someone

 * This may sound strange, but think about it. Minato has it all, he has six Sekireis, all of them are completely loyal (he didn't force any of them). Four of them are single numbers and two of these were in the first disciplinary squad. The other two are Kusano, the last Sekirei, and Musubi, who has the spirit of number 08 inside of her body. He has two of the macguffins, one of which was stolen. He has connections to Yukari, Uzume and Seo, some of the strongest players in the game. Also he is (probably) the son of the Big Bad and The Dragon. He seems much more like a Big Bad then the others.
 * This theory is likely wishy-washy at best... for the manga. In the anime however, it's a different story, as Minaka seems to be deliberately setting up this sort of situation. One person even refers to Minato as a "boss character."

Gaining more Sekirei increases your brain power

 * Minato did get all the answers to some questions Matsu gave him without studying. And he has started to lay schemes for battles.
 * Actually, his younger sister stated that he's quite intelligent, acing his exams through high school. It's just that he's lacking in confidence

Sekirei under go accelerated puberty

 * This would explain the age discrepancey, and how, in 20 years or less, most Sekirei are adults or young adults, with the only exception being Kuu, the youngest. It would be fine except that 01-05 were all awake and adult when 06 and onwards was still asleep and presumably a chibi.
 * Whether this growth is artificial or natural is debateable.

Minato is a "tuned" human -- Sekirei's version of a Coordinator

 * Containing the DNA of both Takehito and Minaka. When she found out that she was impregnated by Minaka, Minato's mom altered the embryo using Takehito's DNA. This would explain why Minato is said to resemble both Minaka and Takehito-- his paternal genetics are half-Minaka and half-Takehito (or whatever is semantically accurate).

Takami is not Minato's biological mother.

 * Despite the fact that Takami and Minato do share a familial resemblance, it also occurred to me at how certain blatantly unrelated characters in this series do as well. Then I started thinking of how oddly Miya acts around Minato, especially the lengths she goes to in order to keeps secrets from Minato. I've also noted how many times those secrets seem to relate to Miya specifically. So the random thought came into my mind: What if Miya is Minato's TRUE mother? Minato is sort of barely young enough to be Miya's kid, depending on how soon she woke up and how fast she formed a bond with Takehito, the timeline is tight but possible. The reason for keeping it a secret is that Minato is a happy, well-adjusted individual when all is said and done, and the Sekirei plan does take its toll on him. So Miya not only would not want to put further undue stress on him, but doesn't want him lashing out at Takami either. It would also explain, if my memory serves correctly, why anybody would be performing tests on Minato specifically (at such a young age anyway). It could also give Miya additional reason for wanting to kill Minaka, as it is likely Minaka would ultimately, if indirectly, be responsible for both the death of her husband, and the theft of her son.

Miya is cock-blocking Minato less for comedic value and more for prevention of heart break.

 * Okay, we have all but confirmed that Sekirei and Humans are genetically compatible enough to reproduce with one another, since modern Ashikabi are descended from the original Sekirei and Ashikabi pairs. Knowing this, and knowing Miya's personal loss of HER Ashikabi/Husband, it's safe to assume that she knows deep in the bone how real a chance Minato's harem has of all getting killed off. She's constantly cock-blocking Minato and his girls not because it's a hilarious gag and it neatly avoids the censors coming down on the series like a ton of bricks, but because she probably knows how much MORE devastated Minato would be to find he's got a kid on the way, who suddenly is dead as well due either to the shear amount of punishment Sekirei's undergo during battle (regardless of victory), or because the potential mother is dead after losing a match. Technically this should go in Fridge I guess.