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.
Naruto: Hinata, could you use your eyes to check me out?
Broken Base: The fic itself has a good deal of people who either outright hate it, or don't think it's as great as hyped. This isn't entirely unjustified - much of this comes from how Alternate Character Interpretation is used, particularly when it comes to making some characters more antagonistic than in canon (mostly the Hyuuga clan); as anyone who's read Harry Potter and the Nightmares of Futures Past might have observed, the author seems to have a preference for the "Black" end of the spectrum when it comes to villains, to near-Stupid Evil levels. While some of this is justified by the nail, said reviewers are of the opinion that he's basically twisting things to suit his own ends (which is, admittedly, partially the point of Fanfiction); basically it depends on whether the story is your cup of tea or not. Few will dispute his talent at writing, however.
As with many Naruto fanfics, readers are also divided on any increase of Naruto's powers or competence, due to concerns that it unbalances the power levels of the setting.
Complete Monster: The author's interpretation of Itachi Uchiha seems to fit the bill. Unlike canon, he committed the Uchiha Massacre simply to test himself (as he originally claimed), but in-story his complete Lack of Empathy makes him one of the most deplorable individuals. In particular, when he crosses the Moral Event Horizon even further by killing Kurenai (showing absolutely no remorse or even emotion at having done so), his partner Kisame Hoshigaki - himself a renowned Blood Knight - is freaked out and disturbed by it.
If Kurenai's theory about Hiashi arranging the annihilation of her genin team just to kill her teammate who had spontaneously manifested a byakugan then refused to join the Hyuga branch family is correct, the Hyuuga Hiashi is without a doubt an irredeemable monster. Especially as she believes the assassination had more to do with Hiashi simply spiteing the Hokage for refusing to force her teammate to accept the Caged Bird Seal.
Family-Unfriendly Aesop: Some of Kurenai's lessons are quite harsh, such as teaching Naruto that some people will simply never accept him, regardless of what he does.
Fanon: Much of the story is based on fanon theories such as an extremely powerful village council and intentional abuse and mistraining of Naruto.
Fanon Discontinuity: Not inside the story itself, but regarding its relationship with canon. Two aspects of the fanfic that are not related to the nail don't match the way they appear in the original series. Specifically: The use of elemental jutsus in chapter 6 is inaccurate, and the portrayal of a certain villain ( Itachi) is very different from how he turned out to be in canon ( that is, Good All Along, for a certain value of good.) Nevertheless, this fanfic was first published in 2006, prior to the manga explaining how elemental jutsu actually worked, as well as prior to certain revelations regarding said villain. On that regard, the author has mentioned that, since he outlined most of the plot since the beginning, the story will not conform to the way things turned out to work in canon, and that the fanfic will stop actively following canon events after a certain point.
As Shino even points out, it made sense for him to do so, seeing as how she broke Tsukuyomi. Of course, this does not stop Shino from entering the mother of all Tranquil Furies.
Actually, since this fic was planned out before certain plot elements came to light, Itachi in Team 8 did this back during the Uchiha Massacre. The above crossing simply serves to assert him as the story's only (so far) clear-cut Complete Monster.
Hiashi does this when he disguises a training session with Hinata to beat her. The rest of the cast is visibly disturbed when they find Hinata battered and bruised, starving, and unable to stand because she hadn't slept at all.
If Kurenai's post-death letter is any indication, Hiashi may also be the one pulling the strings on the incident that killed her former teammates after it was revealed that Kurenai's best friend had the Byakugan despite not being a Hyuuga and refused admissal into the Branch Family.
Absolutely; even Hiashi's biggest Pet the Dog moment from canon (bowing down on his knees to beg for Neji's forgiveness after telling him the truth about Hizashi's death) is replaced by a Kick the Dog moment instead in which he only cares that Neji has lost (despite Neji ending up far more badly injured from his fight with Naruto than he did in canon, the only thing Hiashi is interested in is seeing him punished for "disgracing the clan"). He's easily bordering on Complete Monsterhood.
Also, depending on how indicative Snapped is of the main story, he may well be one of the series' primary antagonists.
Similarly, Hanabi is also quite dismissive of Hinata, a common characterization of her despite appearing in only a few scenes.
This really extends to the entire Hyuga clan, who are in general much, much worse than they are in canon.
Schedule Slip: As of this note, it hasn't been updated in over two years. No longer true, updated as of 09-06-13.
Seinfeld Is Unfunny: Besides the reasons for the Hype Backlash and Base Breaker status mentioned above, part of the divisive nature of this fanfic comes from its age, being first published around 2006. While it's unlikely it was the first one, it's certainly one of the earliest and more notable examples to use certain plot points that have become common in many subsequent fanfics in the Naruto fandom. Among the more used and repeated plot points are: A different teacher training Naruto, resulting in his skills developing earlier; the genin teams being different due to someone else requesting Naruto (and leading to a Naruto/Hinata pairing); and the presence of a sinister conspiracy inside the Village council. While these plot points are actually treated here with more nuance than in many other fanfics, if you have read similar stories and come to this one expecting something incredibly original, you may be disappointed.
Tear Jerker: Hinata. Oh god, Hinata. She is so used to abuse and rejection by her family, she actively looks for a veiled insult behind any compliments she receives from her teammates. She honestly does not know how to react when she realises they're not trying to insult her at all.
The Woobie: Hinata Up to Eleven compared to cannon due to the 'nail' shifting her family life from aloof to outright abusive.
Sarutobi as well. The more aware he becomes of the injustices that Naruto faces, the more guilty he feels when he fails to stop them.
Kurenai, given what we've learned so far about her backstory, qualifies bigtime. As does Naruto, of course... Really, of all of Team 8, only Shino is completely well-adjusted, and given he's The Stoic, that says a lot.
They Wasted a Perfectly Good Plot: Some believe that the death of Kurenai means that many of the plotlines related to her character, such as the death of her old team will never be explored.
Good news! Chapter 22 just arrived and they're exploring it, all right.