* ArcFatigue: While nearly all fans agree that [[spoiler:Miyu's brother]] is indeed [[AlternateUniverseReedRichardsIsAwesome awesome]], some feel ''Drei's'' story arc exploring [[HowWeGotHere his and Miyu's backstory]] has overstayed its welcome. Having gone on for 10+ chapters with any final resolution at least several more chapters away, it's not hard to see why (by comparison, the entire original series ran for just 13 chapters). Making this even worse is the fact that the general details of the story are a ForegoneConclusion.
** As of this writing, [[OutOfFocus Illya & friends have not appeared on-panel for ten chapters]]. Given that Illya is the title character and [[spoiler:Alternate!Shirou]] wasn't properly introduced until just a few chapters before, some people have taken issue with this. Long-time fans have thrown out accusations that [[spoiler:Shirou]] has [[SpotlightStealingSquad hijacked the series]] and the author is [[WolverinePublicity deliberately pandering]] to [[JustHereForGodzilla new fans drawn in by his appearance]].
** Still others are [[DarknessInducedAudienceApathy simply tired]] of ''3rei's'' [[ToneShift considerably more serious tone]] regardless of the characters involved, which the current arc has only [[DarkerAndEdgier exacerbated further]]. Previously, ''3rei'' had paced its more serious drama and action with a plentiful sprinkling of comedy and Fanservice in between, even showing [[spoiler:the Ainsworths']] ([[FauxAffablyEvil Faux]]) AffablyEvil side, and if pacing didn't allow for such breaks there were often [[BreatherEpisode purely comedic side-chapters]] to give the reader a break. In contrast, this story has seen CerebusSyndrome in full effect, being a nonstop TraumaCongaLine for [[spoiler:Shirou]] approaching levels of bleakness that wouldn't be out of place in ''[[VisualNovel/FateStayNight Heaven's Feel]]'' or ''LightNovel/FateZero'', and [[ShooOutTheClowns without a single side chapter and hardly any appearances by the regular cast to break the tension]]. You'd find it hard to believe the series started as a lighthearted love letter to the MagicalGirl genre.
*** Thankfully, the flashback is over, and [[spoiler:Shirou]] even [[LampshadeHanging lampshaded]] how long it was.
* {{Alternate Character Interpretation}}: [[spoiler:The Ainsworths]], especially [[spoiler:Julian]]. Are they a group of [[WellIntentionedExtremist Well-Intentioned Extremists]] or sociopathic monsters willing to abuse a little girl for a plan that might not even work? While their backstory and explanations point heavily towards the former, [[KickTheDog some of the actions they do]] are without a doubt the second. Some fans may sympathize with them, but others share [[spoiler:Alternate!Shirou's]] desire to kill them as slowly and painfully as possible.
* BrokenBase: Illya's extremely bratty behavior towards [[spoiler:Kuro]] in ''Zwei'' turned quite a few fans against her, even those who didn't like [[spoiler:Kuro]] to begin with. Most of the fans her actions upset will point out that [[spoiler:Kuro]] wasn't really hurting anyone, and pretty much everyone except Illya seems to be okay with her presence, making Illya's frequent physical attacks DisproportionateRetribution ([[spoiler:especially since Kuro's curse means she ''can't fight back''). Fortunately, [[MyGodWhatHaveIDone she does get better]] after narrowly stopping Miyu and Kuro from fighting to the death, and the intervention of her mother also helps a lot]].
* CrowningMusicOfAwesome: [=ChouCho=] brought her A-game with the opening theme, [[http://www.youtube.com/watch?v=OBp5XMc-eNA "starlog"]] and the insert song of Episode 9, [[http://www.youtube.com/watch?v=7CS3oZ889M4 "kagami"]].
** Episode 6: [[http://www.youtube.com/watch?v=jiRdixLq38o "Shoujo Shinka!"]] (a.k.a [[spoiler:'''EMIYA''']]) ''and'' [[http://www.youtube.com/watch?v=hGJSdgwtZw8 "Shoujo yo Kate"]] (a.k.a [[spoiler: '''SWORD OF PROMISED VICTORY''']]).
* EnsembleDarkhorse: Even if some fans believe his arc has overstayed its welcome, it almost unanimously agreed that [[spoiler:Alternate Shirou Emiya]] is made of pure awesomeness. Some have gone as far as to claim him to be one of the best incarnations of the character, rivaling if not surpassing even the likes of UBW and Heaven's Feel Shirou, but even Archer himself.
* FoeYay: [[spoiler:Alternate Shirou]] and [[spoiler:Angelica]] has become popular during their fight. The former has some [[ShippingGoggles ambiguously flirty]] dialog along with directly calling her cute. The latter seems to be continually trying to talk him down from fighting and seemed hesitant to kill him.
** [[spoiler: Even more so now that Angelica is revealed to be somewhat similar to Alternate Shirou. Some are even finding similarity between them and F/Z Kiritsugu and Irisviel]]
* GrowingTheBeard: It starts out as a fairly comedic, GenreSavvy series about Illya as a MagicalGirl. It then steadily becomes more serious. The CharacterDevelopment and ArtEvolution become more apparent in its second season, and the gentle amounts of FanService and heavier action clearly show it's a {{Seinen}} series.
* HarsherInHindsight:
** Do you remember the time when Miyu said "brother" to Shirou when she was at Illya's home? [[spoiler: In the universe from which Miyu came Shirou is her brother and Miyu is the vessel of the grail, and he went on a crusade against (very powerful) people who kept her captive, sending Miyu to the universe Illya was from, but ended up getting caught by them and tortured in a dungeon. And she probably remembered about him every time she saw Illya's Shirou]]. Ouch.
** There is also a scene at the end of the 6th episode of the anime (not present in the manga) where [[spoiler:Rin wants to take unconscious Illya home after the Saber card was captured, only for Miyu to interrupt and say that she will be the one to do it. And she carries Illya home while a music box plays in the background.]] Truly a heart-warming moment, but if you know that [[spoiler: Miyu is her universe's Holy Grail vessel and she suffered quite a lot because of it]] then you know why she did it and while it still is a heart-warming moment then, the context changes from "for a friend" to "[[spoiler:for someone who bears the same burden as me]]".
** PlayedForLaughs Illya being a lesbian rapist for Maid Miyu who doesn't seem to mind [[FunnyAneurysmMoment stops being funny]] when you consider [[spoiler: she's an {{expy}} for Sakura from ''VisualNovel/FateStayNight'' who ''was'' conditioned to accept being raped.]]
** Really, just about everything with Miyu becomes this [[spoiler:when we find about about her world and her life with the Ainsworths.]] It starts as early as when she asks Illya why she's fighting. She's not happy about Illya treating collecting the cards like a game, [[spoiler:probably because of how the cards are used in her world, and by who.]]
* JustHereForGodzilla: Quite a number of non-yuri fans intentionally jumped in after knowing that [[spoiler:Gilgamesh appears along with Gates of Babylon, Vimana and Ea.]]
** Likewise, TheReveal that Miyu's brother is [[spoiler:an [[AlternateUniverseReedRichardsIsAwesome alternate Shirou Emiya]]]] has gotten the series a lot of attention from mainline [[VisualNovel/FateStayNight Fate]] fans, especially following the release of [[Anime/FateStayNightUnlimitedBladeWorks ufotable's Unlimited Blade Works anime]]. Even fans who outright condemn this series for its {{Fanservice}} content seem to have nothing but praise for the flashback arc focusing on Miyu's brother.
* LesYay: Miyu develops a pretty obvious crush on Illya, who ([[IDidntMeanToTurnYouOn apparently unintentionally]]) doesn't do a whole lot to discourage it.
** IWantMyBelovedToBeHappy: Miyu gives Illya a day-pass on being a magical girl, and takes on the final card alone, just to spare Illya. This plot unfolds [[AchillesInHisTent exactly as it always does of course]].
** She's desperately trying to ignore it; like when she accidentally kissed Miyu during a dream of Shirou just as she woke up. Miyu didn't mind.
** Illya's Maid {{Fetish}} results in her ''mounting'' Miyu (''Twice!'') before she can compose herself. Miyu didn't mind.
** [[spoiler:Chloe, on the other hand, seems to ''actively encourage'' this. To the point that apparently, she spent the entire time between Chapters 4 and 5 of the second season just going around town kissing girls (Including ''Taiga!''). Granted, she was doing it to drain their mana, but judging by the one we actually get to see, she also took the time and effort to seduce at least a few of them first]].
*** [[spoiler: Then comes Chapter 8 of Drei]].
** [[spoiler:Chloe]] in general with both Miyu and Illya. She managed to make the former unconscious with a French kiss.
** The FoeYay between Rin and Luvia borders on BelligerentSexualTension.
* TheScrappy:
** A lot of Shirou's hatedom carried over from ''VisualNovel/FateStayNight'', but a lot of fans consider him bland and completely superfluous, and don't find the RunningGag of [[ChickMagnet women falling for him]] to be that funny. In addition, there's DieForOurShip at play, as most of the {{Yuri Fan}}s in the fanbase will raise their hackles at any ShipTease he gets with girls, as he's a possible canon threat to ''either side'' of ''both'' [[FanPreferredCouple Fan-Preferred Couples]] Illya/Miyu and Rin/Luvia. [[spoiler:Alternate!Shirou, however, is a MemeticBadass]].
** From ''3rei'', [[spoiler:Tanaka]] is widely hated for being as stupid as one could possibly get without forgetting how to breathe. It hurts that [[spoiler:for her desire to get rid of the Ainsworths, ''which is the only defining characteristic of her personality'', she does almost nothing during the FinalBattle, only giving Illya a long distance powerup]].
* ShipTease: Of the non-Yuri variety
** Gilgamesh: Its hard not to see his teasing of Chloe and Illya as flirting. Double points when he does it toward Chloe when he is naked.
*** This is morbidly hilarious considering his Mainline relationships with their respective characters.
** Shirou: It be easier to list people who aren't teased with Shirou though the most subtle probable goes to Sella up until Her own Sister and Shirou's mother are basically trying to pimp her out to him. In the manga, Rin has the most ship tease. Rin has been the protagonist of many side chapters focused on her relationship with Shirou, that no one else has had.