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.
Broken Base: The Reveal of Shirou's true identity and goals are either a genuinely surprising twist with a lot of merit to it, or an Ass Pull, depending on who you ask.
Cliff Hanger: During the battle between Red Saber (Mordred) and the Homunculus, we never actually see Mordred dealing the final blow. (Only moving in to do so) This leaves a slight chance that something might happen to save the Homunculus from his near-inevitable execution.
And it turns out that the Homunculus managed to survive that encounter when we finally catch up in the second volume.
Shakespeare. While his actual personality hasn't been completely fleshed out yet, what we have seen so far reeks of Crazy Awesome.
The fandom (especially the people on certain Image Boards) has had a soft spot for Astolfo since day one, most likely because of him looking exactly like a cute, pink-haired little girl.
Karna has been popular from very early in development due to his interesting legend, looks and incredible abilities. His Canon Immigrant appearance in Fate/EXTRA made his popularity absolutely skyrocket.
Siegfried is swiftly building a fanbase despite dying relatively early, though it might be the nature of his death and the countless art works of him mostly naked helping.
Atalanta. Like Karna, she was popular from very early on, and her role in the novel proper just elevated this.
Evil Is Cool: Shirou Kotomine, Karna and Shakespeare all fit this trope to a T.
Evil Is Sexy: Celenike Yggdmillenia, Reika Rikudou and Semiramis. Depending on your tastes, Jack the Ripper. For the women; Karna, Achilles, Shirou Kotomine and Shakespeare all fit as well.
Fetish Retardant: Jackie the Ripper's odd body proportions◊ can be this to some people. Basically, she has the upper body of a small, delicate child, but from the waist and down she's a fully grown woman with very wide hips and thick thighs. And that's not even starting on her outfit. Luckily her new and improved artwork from Volume 2 have fixed the worst of this by giving her a normal physique.
Fridge Brilliance: In hindsight, it actually makes considerable sense that a Ruler would be summoned during the third Heaven's Feel. Considering that there was an aberrant Class being summoned (Avenger) and the various outside parties getting involved, such as the Nazis and the Japanese Imperial Army, it wouldn't be too strange for the Greater Grail to call forth a Ruler to make sure the ritual is being guided properly.
Amakusa Shirou being summoned also makes some amount of sense, as he was a native to the country where the third Holy Grail War was taking place.
Jerkass Woobie: Jack the Ripper and Reika. Sure, they have some horrific backstories, but they are also really into killing criminals, or people they perceive as such.
Also applies to Mordred. While she is violent and abrasive, she was rejected by her "father" and had her dreams of being a perfect knight dashed. Not to mention being the pawn of her mother, Morgan la Fay.
Who can Karna defeat? Explanation Due to Karnaīs ridiculous Story Breaker Power and Badassery, People are comparing him to various other Servants, particularly Gilgamesh, and argue whether not he can beat them somehow (Usually itīs a yes).
Fiore wants the horse D Explanation Fiore is shown to have a case of Bodyguard Crush towards Chiron who is actually a Centaur in human guise. Thereīs also the fact that they repeatedly mention Chiron "proving his worth as an Archer despite his human form", which sounds really shady. Fans took this idea and ran with it.
Fiore is Doc OckExplanation (spoilers) Fiore's Mystic Code, the Bronze-Link Manipulators, manifest as five giant Magitek limbs that make her look like a cute female version of the infamous Spiderman villain.
Moe: Fiore, Astolfo, Frankenstein and Roche being the prime examples.
Frankenstein, who gained a lot of hate for being a cute female, when Frankenstein's monster's hideous appearance was central to its story.
Jack the Ripper and Reika Rikudou. Fans are quite ireful of the fact that they are Higashide's Creators Pets who have little to no relevance to the story for any reason other than mercilessly slaughtering people they deem as "evil".
Chiron and Achilles seem to receive a lot of flak for replacing two anticipated servants, Saint George and David. The fact that both of their deaths are basically being telegraphed (Achilles can only be harmed by the divine—not only is Chiron the only divine Black Servant, he uses arrows; meanwhile Kairi is preparing the specific poison that killed Chiron in life) doesn't help matters.
Rescued from the Scrappy Heap: Chironīs personality has saved him from a lot of his previous hate. Achilles's personality has yet to be fleshed out yet, but the hints of a Chivalrous PervertBlood Knight who doesn't ever follow the rules has also bailed him out in the eyes of his previous hate-dom.