lord of the land of fire is an author with multiple Sekirei stories featuring Minato and with different starting Sekirei, updates aren't frequent but has multiple stories already created and finished.
Peeve: Doesn't Write in-depth lemons, search for your squick elsewhere
Synopsis: Author's Summary: Years after his parents survived Heaven's Feel, the son of Kayneth and Sola-Ui finds himself in a different sort of supernatural tournament. But can he survive superpowered alien females, scheming businessmen, and his own partner's urge to strangle him?
Comments:Somehow, Kayneth Archibald El-Melloi and his wife Sola-Ui survived the fourth Heavenís Feel ritual. Their son, Meriwether, seems like a chip offtheoldblock when he travels to Japan to research the Fourth War. Unfortunately, his short layover at Shin Tokyo takes a little longer than expected when he accidentally wings Benitsubasa and gets dragged into the Sekirei Plan. Benitsubasa soon finds to her disappointment that her Ashikabi has lived a rather...shelteredlife. Not that this will stop our protagonist from making the Sekirei Plan a whole lot bloodier...
Synopsis: Honestly, Shirou was beginning to think that he should be used to this — being unwittingly selected to take part in brutal tournament that he had no idea existed until he found himself in the middle of it. Then again, second time's the charm, right?
Comments: Another awesome FSN crossover from the same mind who gave birth to The Hill of Swords. The canon characters of Sekirei are shifted around a bit. There are also some good ecchi scenes. And considering the art style of the Sekirei manga, there will be a lot more. Note that this story had the first two chapters posted within a day of the other; this will probably match the update speed of HoS, so hold on — gab will definitely bring us another great story.
Kazeto: I also recommend this story - it's a nice read and the story actually makes sense (its author puts a lot of effort into researching things). Typos are rare (the only "serious" one was "mpy" instead of "not", and it was kind of funny), and author's grammar is very good. I dare saying that it's better than one of the works it was based on (namely Sekirei), due to the fact that things that should've been fixed got fixed and fan-service isn't so ever-present and is only used as a fun-increasing element in some scenes.
Usandru: While this is technically well written and the author is clearly above average for a fan fiction writer, calling this an actual Nasuverse fanfic is correct only in the sense that it uses the trappings of the Nasuverse to alter Sekirei. If you are looking for something that includes the actual themes and underlying concepts of the Nasuverse, including the creeping sense of horror as the truth is revealed, this is not for you. The characterization of Shirou could also be challenged. All in all, this comes off more as a darker version of Sekirei with a "cooler" protagonist instead of a genuine crossover. The latest build-up suggests that this might change, but it is dubious if this will succeed. Summing up, your mileage might vary.
Zoner16: The story isn't as fast paced as Gabriel Blessing's previous work, The Hill Of Swords, but the tale is both well written and entertaining to say the least. Don't expect to see a lot of Nasuverse regulars, mainly because this is about Shirou being transplanted into the Sekirei-verse, but expect to see them both referenced and discussed a lot. GB does a good job of explaining and crossing Nasuverse mechanics with Sekirei in both a believable and gripping way, allowing those who aren't exactly avid scholars of the franchise to jump in rather quickly. Shirou remains a likeable, yet more mature and well developed character since this is five years later, when he is 20. Some creative liberties have been taken (A couple of Nasuverse characters were made up, but they serve their purpose, and a small amount of Nasuverse lore is incorrect, GB admits that he missed a couple things in research), but overall it is a must read for any Fate Stay Night or Sekirei fan, or even someone just looking for a great story.
Synopsis: A Bleach crossover. Ever go left when you normally go right? Here's one such case, causing a meeting that would not have happened otherwise and whose repercussions will cause many plans to go awry. Here, Ichigo meets Uzume, she makes him wing her, and from there on Ichigo's life changes slowly. Leading a life with a person who claims to be your soul mate can be stressful, in a manner enticing for most people. But Ichigo isn't like most people. The sekirei plan has started — will Ichigo prevail over it?
This crossover is quite beautifully thought out and written. The only problem is that the authors post chapters a few months apart, but I can honestly say they are worth the wait. This fic diverges two years after the final battle with Aizen. With Ichigo powerless as well as he and the human crew about to enter college.
John At Dawn: Something to note here is that Ichigo has no powers. At all. And the author has stated that they have no intention of giving them back to him. So if having a powerless Ichigo is a deal-breaker for you, then you might want to reconsider reading this.
Synopsis: Negi and Asuna thought finding Minato Sahashi in Shin Tokyo would be a simple errand. They never expected to caught up in the Sekirei plan, or the destinies to which it would lead them.
Overlord Zaru: Well written and a bit comedic, Asuna and Negi are in Shin Tokyo before getting caught up in the Sekirei Plan and all of the chaos it brings. It has the potential, not the legitimate thing, but the potential to be as popular as In Flight. Juubi writes like a professional.
Original has been deleted, the author is rewriting it.
Synopsis: Unable to move onto the next life, Uzumaki Naruto travels the world. He comes back to Japan, the place where Konoha once stood, and soon finds himself sucked into a game of battling busty women. It all started when a girl fell on top of him. Literally.