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.
Base Breaker: Many people were kinda put-off by how different Clover was personality-wise in this game from the first installment.
To a lesser extent, Sigma's pervertedness. It's either extremely funny, or really creepy with how insistent he is (plus, Junpei from 999 was far more subtle). Doesn't help that Sigma is actually 67 years old with the mind of a 22 year-old throughout the story.
Alice is seen this way as well, mainly due to her Jerkass attitude in her character path as well as the infamous act where she stealth-betrays you, leaving Sigma with -1 BP (death) unless the player had the foresight to pick betray beforehand. Ironically, outside her character path minus her ending, she is less of a Jerkass and is a helpful ally...when she's not committing suicide due to Radical-6.
Eight Deadly Words: Some people have argued that the cast of VLR are a lot less likable than 999's, to the point where they simply don't care what happens to them all or if they live or not. The exceptions to this are, of course, Luna and possibly Tenmyouji (and, by extension, Quark) if he still has residual points by being Junpei.
This is probably the result of the easy-betrayal system in this Nonary Game, compared to the first one where no one could escape until the end no matter what. Everybody except Luna and Quark will betray you in some ending out of a deep-seated desire to escape, but in 999 leaving people behind usually works against you.
It's also hard to feel the emotional impact of a character's death when you can just go to a different timeline and save them, especially since it's precisely their death what leads to the eventual Everybody Lives
Ensemble Darkhorse: Luna, because she is by far the nicest and friendliest person in the cast, to the point that she never betrays you. This is an especially notable dark horse since traditionally feminine, submissive characters USUALLY tend to be unpopular in the West.
Fan Dumb: Some European fans complained that their version will be Japanese dub only, never mind that they should be lucky someone even considered an EU port for VLR when 999 was never released.
Harsher in Hindsight: In a lot of the bad endings, someone manages to escape and then promises to contact the police to come and save everyone else left behind. The problem is, as you play through all the routes you gradually learn that the world is now post-apocalypse...as Tenmyouji (who knows about the Radical-6 pandemic) snarks in his own first bad ending, let's hope there's someone left out there to contact for help...
To say nothing about the fact that you're on the Moon.
And, as all the characters are also infected with Radical-6, any non-cured character still alive after any ending will eventually commit suicide due to the disease. Essentially, any ending excluding the true one would end up like Clover’s ending.
Betraying Luna, as Sigma is unknowingly her creator and Luna herself has quite a bit of angst relating to the fact that she's not human.
Player Punch: The game definitely makes you feel like a jerk any time you choose "betray", but it's especially bad if the opponent is Luna or a comatose Quark.
Learning that the dead old woman is Akane.
That One Level: The dice puzzle in the Q Room. Unlike the same puzzle in the Archives, it's not enough to have the right number on the top of each die, they also have to be aligned properly, which requires a specific combination of moves for each die.
Ship Tease Sigma could reasonably be shipped with every single named female character in the game, since to get the Omega Ending he must be emotionally close to each one of them in at least one timeline and at least one of them is strongly implied to have feelings for him. Can reach squick territory after the reveal.
The Untwist: Dio is so repugnant that finding out he's the antagonist of the scenario is...really surprising because it's so unsurprising. You keep expecting him to have some sort of hidden redeeming value. Nope. He doesn't. He really is as bad as he appears to be, and then some. Particularly surprising in the sequel of a game where the biggest jerkasses turn out to be caring and selfless people
Accordingly, Quark is such an innocent and well behaved child and Luna such a nice and caring woman that anyone who played the first game will become immediately suspicious and may even for a while believe Dio's story that Quark is the one who picks "Betray" against Tenmyouji. They turn out to be, respectively, even more adorably innocent and heroically selfless than initially apparent
The True End, for some players. If you know prisoner's dilemma, then you know from the start of the game that there's only one way for everyone to survive: cooperate. Unlike 999 and the "Q/9" twist, VLR has no way to disguise this.
Woolseyism: The game's Japanese title was generally translated as Good People Die, but it also could be read as I Want To Be a Good Person. To preserve this double meaning, the English title was changed to Virtue's Last Reward to play off the phrases "Virtue is its own reward" and "The last reward" (death). The scenario writer liked it so much he had the game's main theme on the soundtrack renamed to "Virtue's Last Reward".