FanficRecs Read if you like Sekirei; avoid if you like Rin and/or Saber
This is a definite YMMV, considering the most recent chapters. As many FSN fans have pointed out in the reviews and fic forum, there are serious flaws in Rin's and Saber's character portrayals.
Along that note, if you are a fan of the Sunny Day end and/or the Shirou/Rin/Saber ship (anyone? no? just me?), I would avoid this like the plague despite it ostensibly starting off from both (for... no clearly discernable reason other than making Shirou into a comfortable-with-polyamory Counter Guardian EMIYA Lite borderline Stu). It basically takes a huge dump on everything good about that ending and that ship and tries to write it off as taking the intellectual high ground about "harem deconstruction" by ruining the relationship Shirou's actually fucking worked on while leaving his convenient-stand-in-for-therapy psychic alien harem that he picked up by accident intact. Um, how the fuck is that deconstructing anything about harems aside from the "people integrating seamlessly" thing?
But I mean, if you like having in the same chapter a heartbreaking clearly-meant-to-be-permanent breakup scene AND rebound sex during which the protagonist is thinking about how happy he is with his new relationships, and this doesn't strike you as horrible whiplash and totally OOC, go for it.
FanficRecs Hill of Sword's Spiritual Successor?
Hill of Swords was rather fast paced, completing its run in a meager 23 or so chapters. It combined wonderful characterization, amazing dialogue, and events didn't seem forced or out of place. It's also possibly the most famous example of YMMV fic.
As with Ho S, the fic is extremely YMMV. It isn't that focused on action, more on the slice of life. Coupled with slow updates, snail's pacing, and its extreme length, it's not for those who were accustomed to Ho S's fast pacing.
It counts more as a Sekirei fic than anything else; it can't count as a Nasuverse fic since the only aspects present are the Clock Tower (which isn't taking its role as an antagonist seriously), and Shirou and his experiences. The characterization doesn't seem to be that well either in regards to Shirou. Sure, Rin and Saber show up, but for a meager two chapters before they're gone, possibly permanently.
However, it's amusing to read in some places and has long chapters and good grammar to enjoy.
FanficRecs By 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.
FanficRecs By 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.
FanficRecs By Kazeto
I 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.
FanficRecs captchacritter
No matter how good or bad or boring this story might get, you all can at least take heart in it that its still way, way, waaaay better than Sekirei canon is. And really, isn't that what matters?