These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: In Flight
Alternate Character Interpretation: Ironically (and interestingly), Lancer is one of the few Grail War opposing participants Shirou has both a relatively good opinion of and who he doesn't condemn for his actions. Compare those GB reckons Shirou must dislike: Shinji, Gil and Kirei are pretty much his mental Butt Monkeys, the former two so disliked they're the only people he'd not feel sorry for if they had Homura's condition (though in Shinji's case Shirou notes that it would be somewhat of a karmic punishment.); Rider he didn't see enough of to see her good sides; Archer he considers to be trying to haunt him; and for Caster, he reserves a Precision F-Strike. Just ...
Angst? What Angst?: Shirou and Musubi are both disturbingly chipper and blase about the horrific near-death experiences they endured in childhood. The people around them consider them "distorted". Shirou is freaked out by how cheerful Musubi is when she says that she was dissected as a child and wonders if that's how other people feel when he talks about the fire.
Broken Base: The Twenty-Eighth Wing divided the fanbase between those who thought it was a small slump in quality (having come after a hiatus of four months) and those who consider it perhaps the weakest chapter to date (forvariousreasons). The story itself becomes that much more divisive as time passes, really - almost anyone thought the early chapters were excellent, but as the particular type of story becomes clearer to them, more of them are dissatisfied.
The whole "Emiya Clan" deal - either you love it for the Mary SueMemetic Badass Shirou, or those reasons make it the worst thing that ever existed. Given that even GB has admitted that he tries to avoid Shirou being invincible (whether he succeeds or not is a matter of opinion), there will never be a single opinion about the fan-made concept.
Chapter 41 has led to a mass exodus of readers from the fic, many having seen Shirou's reunion with Rin and Saber as underwhelming and the conclusion, with Shirou winning the battle with Saber far to easily, and defeating Rin using what, in Sekirei canon, amounts to a joke technique, followed with him geas-ing Rin into never being able to see or interact with him again in order to prevent her from chasing him, then promptly followed by him waking up a few days later almost completely healed, and despite the fact that he had just broken up with Rin and Saber not three scenes before, immediately having sex with Kazehana all while gushing about how his relationship with his psychic alien girlfriends is so much more fulfilling than his relationship with his old girlfriends, not even minding the fact that Rin and Saber will both probably become self-destructive wrecks having been abandoned by him as the straw that broke the camel's back. Their reconciliation with Shirou in the final chapter has softened the opinions of some detractors, though.
The reconciliation made it even worse actually. Many readers (and not just those on Beast's Lair) saw this as proof that GB's version of Shirou was meant to be some kind of Memetic Sex God who gets the full harem route from the beginning, thereby partially supporting the whole Emiya Clan idiocy. Seeing how Shirou manages to wing almost every single major character anyways, it's little wonder that most people saw this as a weak Ass Pull meant to fulfill a fantasy rather than an actual conclusion.
Foe Yay: Shirou and Karasuba. This is probably what caused her to react to him.
"Funny Aneurysm" Moment: Miya says that why Shirou can't do something for her to properly punish him. Well, when she finally does so, She's been blasted thorugh a wall by a Fraga clan member and half of Izumo is torn. Could count as Hilarious in Hindsight if you're mean.
As of the 27th wing, we learn that the male Ashikabi of MBI Disciplinary Squad Sekirei has taken a romantic interest in Shirou; particularly after he learned that one of Shirou's Sekirei is (or is it was, now) male.
Mary Sue : Not so much in-story, he is just a skilled man who has a rough time. But in the Emiya Clan fan-stories and the Omakes, the fandom make him taking several hundred of GAR levels.
Jerkass Sue: Shirou. He behaves like an ass towards everything and everyone who disagrees with his view on life, and he's constantly forgiven within twenty minutes. He has superficial angst and self-hate, talking about how "cursed" his life is, and then promptly dumps Rin and Saber in the most horrific fashion possible, making the former completely unable to see, speak, or interact with him in any way ever again, then is forgiven by them twenty minutes later at which point they leave without incident, and then he goes back home and has sex with Kazehana two days later, despite the fact that his arm was cut off in his battle against his former girlfriends. He also somehow defeats Saber in a swordfight, despite everything in Nasu canon outright stating that that is impossible for him to do, and has never lost a single on-screen fight during the course of the story. Yeah, Sue doesn't even begin to describe this guy.
Memetic Sex God: Shirou is one in the making but not officially GAR yet. Just one Tantric Ritual turns a scrapped Sekirei into an official Sekirei. It worked for Akitsu and Yume.
Rescued from the Scrappy Heap: Shirou's previous landlord. In the manga he was a gruff and unpleasant old man, who kicked Minato out of his room almost out of spite. In the Fan Fic he turns out to be a relatively decent though still gruffy fellow, giving Shirou a week to find a new place, offering him a job with good pay, recommending him to his fellow landlords, and even paying him more than they agreed on.
The Woobie: Akitsu. Since winging is a "mating ritual", as Shirou put it, being a scrapped number means that Akisu can never find a true "mate" for herself. Considering that the Sekirei believe the person who wings them is their soulmate, this essentially boils down to her thinking that she will never be able to find love. Thankfully, Shirou was there to help her out.