Dr. Breen's speech in the early levels of Half-Life 2 raises an interesting point about the nature of immortality and the responsibilities it brings. This may actually have been the writers' intention, as it's common for villains to use reasonable arguments to justify unreasonable actions, even in Real Life. All is moot on the ground that he's working for an interdimensional empire that has killed and enslaved countless billions and drain Earth (and many other worlds) of much of its natural resources, oh yeah and suppressed breeding. On the other hand, it's hinted that if Breen hadn't arranged for Earth's surrender, the Combine would have completely wiped out humanity. Whether Breen is a sycophantic power-hungry quisling or a deluded guy who honestly believes his propaganda about the "Universal Union" that the Combine bring is a subject of much debate.
No matter what character interpretation you may subscribe to in Final Fantasy Tactics Advance (whether or not you see Marche as a Villain Protagonist), it's hard to argue with some of the justifications that both sides use. If you believe that Marche is in the right, the royal forces (who are attempting to stop Marche from destroying the crystals and returning to St. Ivalice) are very correct when they claim that he is destroying the one place where his friends and brother are happy. On the other hand, even if you see Marche as a dangerous Jerkass, he is still right when he claims that Mewt and Ritz (among others) are using Ivalice to avoid facing their real-world problems (and because the Ivalice world actually replaces St. Ivalice instead of existing separately, they are forcing other people to cease to exist in the process). Basically, no matter who the player personally supports, the "villains" are correct when they call the "heroes" out on their selfish attempts to impose their own form of reality on the world. Needless to say, intepretations on who was "right" are fodder for much debating.
The Jackal from Far Cry 2, on his interview tapes, sounds a lot more logical than the game seems to want you to think of him as, given the tape descriptions. While many of them are blatantly MORALLY wrong, his logic to justify what he does makes a scary amount of sense. This is especially invoked in the tape asking him why Africa, when he gives the interviewer a small Hannibal Lecture, asking him if there's someone else's home he doesn't care about that he should sell weapons in.
Mass Effect 3: During the meeting with the Council after escaping Earth, regardless of which one it is, they shut down Shepard and Udina's alliance argument with the pragmatic fact that with the Reapers focusing on Earth, they can use the time they have to start defending their own borders. The game treats this as a selfish act typical of the Council, and a sign that they still view humanity as expendable despite years of them attempting to prove themselves to the galaxy, but when one really thinks about it, it's hard not to see their point. Many fans have been annoyed with Shepard's obsession with Earth, pointing out that Earth isn't the only important planet in the galaxy and that it makes sense trying to save what can be saved and pile resources instead of wasting them trying to regain lost causes. While Shepard and Udina are absolutely correct that they need to work together, it doesn't give them the right to dismiss the Council as misanthropic and cowardly just for looking out for their own people.
Bully features a feud between the Math and English teachers. Mr. Hattrick, the Math teacher, is a tyrannical monster who uses his wealth and connections to bully both the students and the other teachers with impunity, whereas Mr. Galloway, the English teacher, is kind and mild mannered, and has been bullied by Hattrick for so long that he's turned to alcoholism. The problem here is that Galloway actually shows up to class hung over and even drinks during school hours. Hattrick catches him at it and tries to get him fired. The game itself presents it as Hattrick Wrong Galloway Right because it fits in with its themes (In particular, that people in positions of authority are oblivious to what is and isn't actually Harmful to Minors; the students are aware that Galloway drinks, but it doesn't offend them or encourage them to drink themselves, while Hattrick is a classist bully who maintains a clear-cut appearance to keep anyone from suspecting him). But, regardless of the reason he's drinking, firing a teacher who shows up to teach drunk makes more sense than just brushing it off as "a chap can have a drink when he bloody well wants". In Real Life, any teacher who did that would be in serious trouble.
As time goes on in the Mega Man X series, the games start leaning heavily on the idea that it's far more the mistrust of the humans and the trigger-happiness of the Maverick Hunters that are causing everything to go wrong than it is because of the Mavericks themselves. But considering that Mavericks, both infected and free-willed, have started multiple genocidal wars because they have a gross misunderstanding on how evolution works or are flat-out insane, or find the act of provoking a shooting war to be preferable to clearing their own names for the sake of honor, is it really any wonder that the population at large doesn't trust them?
Channel4's game The Curfew is meant to be a look at the oppressive checks and Orwellian surveillance instituted in a hypothetical UK in the year 2525 by the Shephard party, where most are legally bound to be in by 9PM, and immigrants have to earn "citizen points" before becoming citizens, or moving from citizen Class B to the privileged Class A. The player's job is to listen to and play through the stories of the four people they're stuck in a hostel with so they can figure out which to give information that might topple the ruling regime. While the question of what human and civil rights are and should be is an interesting one, the event that propelled the party into power was a major, catastrophic nuclear attack on Great Britain, which had been preceded by a major economic depression. The titular Curfew is aimed at preventing another such attack.
Faldio is a strawman for advocating the use of the game's parallel of WMDs, which the game is staunchly against. The problem is that he was right. Forcing Alicia's Valkyria powers to awaken is the only reason Gallia is still standing by the end of the game, because on at least two occasions, when the situation was the most dire, they saved the day. Faldio is treated as a power-hungry monster and no better than their enemies, but that doesn't change the fact Gallia only won the war because of precise application of the weaponry the game's Aesops condemns.
In Faldio's case, an additional problem was with the fact that he was treating Alicia as a weapon to be used against Gallia's enemies, not as a person who has feelings and free will — which is, incidentally, the same way Maximillian was treating Selvaria. This varies somewhat between the English and Japanese versions; the English script implies that Faldio didn't ask nicely because he just couldn't risk the answer being no, resulting in an I Did What I Had to Do scenario. The Japanese paints him as much more sinister.
The anime version throws in UST between Faldio and Alicia despite being based on the Japanese script, slanting his motivations in the English script's direction to a degree.
In the dev's effort to discourage piracy, Hyperdimension Neptunia Mk 2's villains sometimes take a more sympathetic stance than the heroes. "Hey kid, want a mod chip? You'll be able to do things like cheat!" "Don't listen to her! Isn't it more fun to play the game as the devs intended it to be played? Good kids obey authority!"
It comes to a head, or at least a more balanced light, during the rematch with CFW Brave. He and Uni have a pre-fight debate in regards to the importance of making children happy vs. the integrity of happiness through underhanded means. Both sides raise understandable points and despite Brave inevitably losing the resulting boss battle, both of them end up respecting each other and their goals.
Used deliberately in Pokémon Black and White, since the plot is a Decon Recon Switch of the "cute monster pitfighting" premise. The enemy Team is a Pokemon rights group trying to have said pitfighting activity banned as abuse. By, you know, mugging Trainers. Some members are portrayed as extremely sympathetic, along with their figurehead leader, who is recognized as a hero by the Powers That Be for his efforts in Pokemon liberation. The others kick wild Munna.
Team Plasma's perspective on things is even more understandable if you play by a Self-Imposed Challenge whose rules dictate your Pokemon are Killed Off for Real if they get KO'd, such as the Nuzlocke Challenge.
A critique of Injustice: Gods Among Us. While Superman's methods are wrong, neither the game or the tie-in comics are ever able to fully refute Superman's arguments. Batman has no viable alternative to killing supervillains, nor any real interest in redeeming them (it being Green Arrow and Black Canary that set the stage for Harley's Heel Face Turn) or averting Cardboard Prisons and can never say what is so bad about killing the Joker. While the Regime took it too far, it's inarguable that they were addressing very real problems in DC's universe that Batman didn't appear to have any real interest in fixing.
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