Brick Joke: "Alright, Root. That does it. All the other stuff, I could handle in time. But now I have to worry about having unauthorized porn of me circling the country as well?" This gets even funnier when you've read In Flight.
Cargo Ship: Shirou's reaction to Derflinger had shades of this.
"Shirou," Louise said, her eye twitching, and her fists clenched as she eyed me strangely. "I'm glad you like the sword, but could you please stop rubbing your cheek against it? It's disturbing."
The Zero Fighter too. No wonder no woman can seduce him his love is only for weapons of mass destruction
"I gave into the urge myself, and embraced the machine guns. "Oh! The armies we'll slaughter together!" I crooned, rubbing my face against the weapons."
'He had invited me to his room after his shift was done so we could discretely begin working on the book in privacy later that night.'
Love It or Hate It: The fandom loves it because they see the alternate familiar as much cooler than Saito, while the hatedom hates it because they see Shirō as mischaracterized and think the fandom hates on Saito too much.
Some of this is addressed in the author's notes at the start of each chapter, mostly concerning whether Shirou is overpowered or underpowered compared to his Fate/stay night self, the relation to Fate/stay nightCanon (which the author clearly explained as being an alternate universe where parts of the the Unlimited Blade Works route seeped into the Fate route so the author could use a Shirou x Saber pairing while having UBW's better character development and magic for Shirou), and some admittedly Out of Character bits (Shirou has never sworn on the Root or really said much at all about the Root of the World in the entire Fate franchise so fans of the Visual Novel find it off-putting).
The debates over whether this Shirou is overpowered or not largely center on the Final Battle and how it kinda sorta totally breaks the rules of the Fate setting in half. In order, Shirou...1) uses Unlimited Blade Works (which he doesn't have anywhere close to enough mana to use and required a huge donation of mana from Rin to use which he doesn't have here), 2) uses Avalon inside UBW (while Shirou can project a perfect Avalon, it only works using Saber's mana and would be completely useless unless he had an active contract with Saber), and 3) uses Excalibur (even if we assume it is Excalibur Image - an incomplete version since he can't Trace the real thing - actually using it would kill him instantly as he doesn't have enough mana.