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.
Miboshi is a Creepy Child appearing member of the warriors of Seiryu who is truly far older than he appears. Miboshi's MO is to possess his victims and turn them against their friends, forcing the friends to experience the pain of betrayal and delighting at the agony he causes to his host by forcing them to harm the ones they love the most.
The Emperor of Kutou acts as the commander of the Big Bad Nakago until Nakago opts to overthrow him. We soon learn the reason that the villainous Nakago always hated him. A sleazy Smug Snake who sent his armies on campaigns of extermination and conquest, Nakago saw his people slaughtered and his beloved mother being raped by the Emperor's soldiers before his powers awakened and he accidentally killed her and the soldiers. The Emperor decided to use Nakago as a tool from then on, knowing his potential. Captivated by his beauty, he opted to keep him as a Sex Slave as well despite Nakago being only a little boy.
Creator's Pet: Nakago. To the point that this is on the YMMV page only due to formality, since as mentioned before, Yuu Watase herself confessed he's her favourite character and tended to favor him because of it.
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...
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.
How about Miaka's brother Keisuke with Tamahome? Just look at how the former gushed at the latter once he woke up.
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: Miaka's hatedom just loves to do this to her so they can pair themselves/their Mary Sue with Tamahome instead.