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.
Nakago can be your average revenge-driven Big Bad, or he can be mentally unhinged. The second is highly plausible, considering what he had gone through.
Angst? What Angst?: Miaka shows remarkably few psychological aftereffects from the multiple sexual assaults she endures over the course of the series, although one could argue she expends enough angst over Tamahome that she doesn't have any left to spare.
Draco in Leather Pants: Nakago has done atrocious deeds, but lots of fangirls love him and handwave his evil actions just because he's OMG SO PRETTY. The fact that he's Watase's personal favourite character doesn't exactly help.
Suboshi also gets this treatment due to several woobifying events in his background. His more rabid fans seem to think that the fact Nakago manipulated him means that he can be absolved of any real fault for his murder of Tamahome's family...
Fanon Discontinuity: Eikou Den and the first OAV series are basically regarded as non-canon by fans. The character novels are also highly unpopular with fans, largely due to accusations of retconning.
Fan Preferred Couple: Suboshi is far more popular a love interest for Yui than Yui's canon boyfriend, Tetsuya.
Ho Yay: Nuriko's feelings for Hotohori and Tomo's for Nakago, both canon. Plus the aforementioned Tamahome/Nakago Foe Yay.
And there was apparently enough Tasuki/Nuriko going on that they became the basis for one of the earliest yaoi doujinshi out of the gate. It doesn't really help either that their Englishseiyuu got married.
Suboshi/Amiboshi, even lampshaded when Miaka sees them together and compares it to a romantic movie with the same person playing both parts.
There's also that scene where Taka and Tasuki inexplicably go take a nap together.
Moral Event Horizon: Suboshi violently murdering Tamahome's father and little siblings.
In Eikou Den, Mayo stealing Miaka's unborn baby and trying to erase her from existence.)
Narm Charm: A lot of moments in the English dub of the anime come across as either of these two. The main two that come to mind are episodes 4 and 5 of the second OVA: Tasuki's Near Rape Experience with Miaka is dramatic until you remember what other roles Daran Norris has had, and Hikou's death is an absolute Tear Jerker...right until you hear the sound effect they use. In fact, the whole scene can be seen as Narm because of the music they're using.
Ron the Death Eater: Oooooh boy...Miaka's hatedom just loves to do this to her so they can pair themselves/their Mary Sue with Tamahome instead.
The Scrappy: The anime's portrayal of Miaka tends to get her slammed as a Purity Sue. The manga portrays her in a more realistic way. Ironically, MayoSakaki from Eikou Den fits the Mary Sue bill more, technically speaking, and actually replaced Miaka as the Scrappy in the eyes of some fans with the release of Eikou Den. Ashitare, Yui and Tomo have also gained a degree of Scrappydom.
In fact, Miaka is one of the most hated female characters in anime/manga — to the degree when fans used a "Level of Suck" meter to measure other shoujo heroines. "At least she's not a Miaka".
Villain Sue: Nakago, if you ask a good chunk of fandom.
