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.
Arc Fatigue: The Final Boss from Disc 2 is fought once again in Disc 3 with a similar moveset in a similar area and even an Avatar battle afterwards.
Alkaid. One half thinks she's The Scrappy, the other half is in love with her.
Shino might count as well, since some think she's a complete bitch, and others love her.
The R:2 saga in general.
Best Boss Ever: In Vol.3 many people agree that the final battle against the Three Azure Knights, Aura Knights, is the best boss fight in the series: fought at Hulle Granz Cathedral, awesome music, it isn't an avatar battle and merely the fact that you are fighting three of the main heroes from the first quadrilogy of .hack games.
Complete Monster: Sakaki was merely annoying and overzealous at first, but later revelations removed any kind of sympathy fans might have had for him. Specifically, the revelation that he had been manipulating and controlling AIDA behind the scenes, and that his ultimate goal was to use AIDA as mass mind control over all of humanity. But the biggest blow against him was his treatment of Atoli, who had long been one of his strongest supporters. Turns out he had met her on a suicide website, preyed on her fears about being alone and considered worthless, effectively brainwashed her into depending on him, and then Mind Raped her to bring out the power of her Epitaph. When all of his plans fail and he gets infected with AIDA himself, he then spends the first half of the final volume putting together a sadistic tournament for the sole purpose of making Haseo and the rest suffer (harming quite a few others in the process), and laughing at the pain he's causing.
Critical Dissonance: Most Critics gave GU a Low to Medium score, most who have played love the game to the point of giving it high to perfect scores. Mainly due to the "fresh" gameplay compared to the older games, as well as more likeable characters and story.
Crowning Moment Of Awesome - Too many examples to list. Haseo's arrival as a PKK in Volume 1, the four-way Avatar summoning sequence against Sakaki's AIDA, Atoli telling off Sakaki after he betrayed her with Mind Rape...
Alkaid was originally slated to only have a brief appearance in Volume 1, but fandom demand and the creator's preference changed that.
Disappointing Last Level: After testing Skeith's ultimate form, the rest of the Final Boss fight is done with the regular playable characters. Futhermore, most of the next fights against doppeldangers and the final one will barely pose a challenge if the player already defeated the doppeldangers from Disc 1 and 2.
Fridge Logic - How come no one ever brings up ripping off their headset or unplugging their PC?
In the R1 games being anywhere near one of the phases made players begin to have spastic fits such that they are physically unable to take their hands off the controllers unless there's someone in the room to do it for them, like Mai and Tokuouka in the first volume of Liminality. The same possibly holds true for anyone in the presence of AIDA or the Avatars.
Why do Atoli's parents take her to the doctor, confirm she has Doll Syndrome, and still let her play on the computer?
The answer to that could be Fridge Horror. We later learn how isolated Atoli is and it's heavily implied from her pre-avatar battle that her parents are at minimum neglectful.
If Aina was so sick in the hospital, why did doctors allow her to play an online virtual reality game so much?
Game Breaker - The Doppelganger Items and the pair of guns that Haseo gets in the Forest of Pain.
This also includes Haseo's ability to juggle enemies with his guns, semi-infinitely if the player is quick with the reload button.
And don't forget the DG-Y's ability. Combined with Super Charge, it essentially eliminates Skill Trigger recharge.
Quick Rengeki or Jet Speed Attack + Awakens also fits in this trope.
Awakenings are so broken that people have actually complained about how gamebreaking they are.
Starting a new game in 1 if you have the clear data for 2 on your memory card allows you to start the game at level 35 even after being Data Drained. For the record, the PKs who kill you at the start of the game are level 10, and the crazy bitch Bordeaux is only level 27 when you have to fight her in the arena. It's possible to beat every single mission up to the battle with Alkaid without having to level yourself up at all. But be warned, your allies will be horribly weak.
There might be a reason why you are the only who can use a Broadsword in your party: even all by yourself you can juggle most small sized enemies and "player" enemies until they are dead or enough to finish with a Skill Trigger.
Damage Change + SP Regen could also be considered a Game Breaker, although to a lesser extent. It's pretty damn easy to break this game.
Atoli can become one. Damage Change, SP Regen, Skill Boost (for Rig Geam, which stacks with SP Regen), and Dancing Haze combine to create an unstoppable wall. Atoli is the only character that can use Dancing Haze - and it gives a 2-slot armor customization that may very well be one of the best caster customizations in the game, on a weapon. If she somehow takes some form of physical damage, she's able to heal herself almost immediately afterward.
Haseo also has some moments with Ovan that gets even more intimate in the manga.
And dear God, Piros the 3rd. "Your love makes me hot!" Also another case of Do Not Want for Haseo.
Kuhn as well. Send him the Flower Gift card and he'll think Haseo is hitting on him.
Silabus, again with Haseo. Some of his e-mails suggest a stronger devotion alongside his obvious admiration, and his Promise Card scene is rather...interesting. It should also be noted that Silabus could be considered a Spear Counterpart of Atoli, the closest the game gets to a canon love interest.
I Knew It: Prior to the release of Redemption, some people had already been speculating that Sakubo was one person with a split personality.
Also, there were multiple theories regarding the true identity of Tri-Edge before Reminisce was released.
Nightmare Fuel - The Dopplegangers. When one shows up on the map and notices you nearby, it starts to slowly and confidently walk towards you while an increasingly scary music that alerts you of your impending doom starts to play and grows louder the closer it comes toward you. The screen also starts flashing red, and more so when the enemy closes in on you.
Entering in a battle to escape from it is useless like when you get to fight P Kers he'll, literally, walk in with his shady appearance.
Skeith beating the hell out of Magus in Volume 1. Haseo panics.
Sakaki mind-raping Atoli may count too, considering Atoli's reaction makes it seem as if she's being literally raped.
Obvious Beta: vol.1 to the sequels. The combat system is a bit different and slower than the sequels, the steam bike is very slow, hard to maneuver and far from useful, there are some options that were scrapped altogether in the sequels, only weapons can be alchemy enhanced, there's the infamous bugged area that allows for fighting a vol.2 enemy that drops vol.2 items, and so on.
The Scrappy - Piros the 3rd is generally agreed as this. Several others can fall into this trope as well.
That One Boss - AIDA <Oswald> in Reminisce. It has several difficult to dodge and very damaging attacks that can easily rack up about 1/5 of your entire life bar and if you get careless you might get hit many times on a row.
AIDA <Victorian> in Rebirth. Destroying its protection isn't (quite) the challenge, Data Draining it is. Victorian moves erratically all over the place while spilling bullets that will cancel your Data Drain gauge entirely if one so as much scratch you. Failing to Data Drain it in time means the boss will have around 1/3 of his life back in a battle that might have taken about half of yours.
Cubia, as well, at least in the Avatar Battle portion. It's not so bad until near the end, when Cubia whips out it's strongest attack, Chaos Gehenna. This is even considering that Cubia is the Final Boss and technically you're fighting it's first (two?) form(s), and that ONE SINGLE ATTACK can easily send you back to the very start of what is already a long battle.
Unfortunate Implications - It's encouraged that it's better for Saku to remain a split personality of Bo, instead of being reabsorbed by his mind. Real cases of dissociative personality disorder can attest how problematic this is. However, there also exist cases where the premature reintegration of the dissociative identities of the individual can be just as harmful to their psyche, as they are not prepared or ready to "part" from the other identity.
Wangst: Haseo gets a lot of this in the first game especially when he throws angry tanctrums at Atoli for enjoying the game. It is far more exaggerated in the manga and the CGI film when Haseo is given so many creepy expressions that he looks like a molester.
The Woobie - Several. To name a few, Atoli and Sakubo.