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.
Broken Base: Much less broken than other examples, but there's some debate over whether it's an Even Better Sequel or a really good follow up that doesn't quite match the previous installment. While some prefer VLR's new mechanics and greater scope, others prefer the more focused narrative of the previous. The characters are a frequent point of contention, as many see VLR's cast as primarily a bunch on Jerkasses whereas the cast of 999 had its share of Hidden Depths.
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.
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.
Fun with Acronyms: Meta-example, but the acromyn for Virtue's Last Reward can be read aloud as "valor".
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...
Not to mention THEY'RE ON THE MOON! It'd be lucky if they ever saw another human being at all!
Made better by the fact that, somewhere on the moon, there are 8 other Rhizomes, presumably filled with people that escaped from Earth.
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.
Narm: K's "shocked" animation pose has him clapping his hands to face not entirely unlike the iconic Home Alone cover. His pupils turn vertical too. It looks more silly and adorable than shocked.
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.
Some fans has expressed their dislike of Alice and Clover whenever VLR comes up on various forums. Ironic since Clover at least was brought into the game because she was a fan favorite in 999.
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.
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.
Uncanny Valley: Clover falls into this with her unemotional perpetual grin mixed with the soulful voice acting she can come off as quite creepy. Her actions don't help either.
Some people feel this way about Luna as well, due to her stiff movements and occasional monotone voice. This becomes a bit of Fridge Brilliance following The Reveal in her route
Unintentionally Unsympathetic: Phi is something of a secondary protagonist, but she urges you to betray in the first round, even against Luna, even after mentioning that the best way to win the Prisoner's Dilemma for the whole group is to ally. And if you take her advice and betray, she blames the vote on you. If you ally and you're right to do so, she still chews you out.
What an Idiot: You've just inspected the Laboratory with Dio and Clover, found Axelavir in the safe, and had Dio steal it from you, who tells you to vote Ally in the next AB Game and tell nobody that he has it, or else he'll smash it. You'd expect: Dio to stay where he can see them and hear what they're talking to the others about. Instead: He leaves their side no less than three times Even Worse: He goes into one of the soundproof AB Rooms prematurely, leaving Clover and Sigma with everybody else, and no way for him to know if they tell the others about the Axelavir You'd Expect: Sigma and Clover to tell everyone, especially the physically intimidating K, that Dio stole the Axelavir, and perhaps ask K to grab and search him after he leaves the AB Room Instead: They never do this, and they're forced to risk either Sigma dying, or Quark to never have any hope of being cured from Radical-6
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".
Myrmidons were originally called Clay Dolls, another way of saying golems. It is implying that Dio and the other Left clones are similar in nature to the gaulems. Myrmidons on the other hand are a reference to "ant people" from Greek mythology which also suggests that while autonomous, they are a hivemind like the gaulems. It also has a double meaning as "fanatical warrior".