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.
For the SC1 and Brood War subjective tropes, go here. The SC2 subjectives are here.
The series as a whole
Broken Base: Examples include elitist "progamers" vs "casual gamer noobs"
Complacent Gaming Syndrome/"Stop Having Fun" Guys/The Social Darwinist: Apparently the tactics to playing the game in Multiplayer are set in stone. Trying anything new would result in the game quickly ending for you and/or your allies shunning you. Also, some of the seasoned players do not take too well to being teamed up with new players, even going as far as to verbally abuse the newbie and even bullying the newbie into leaving the game, by means of attacking the newbie's base, despite the newbie being an ally.
Kerrigan's hated instructor, Lieutenant Rumm, forced the young girl to use her exceptional psionic powers by injecting a kitten with a tumor-causing chemical, and gave her the option of destroying the kitten's tumor or euthanizing it. Not willing to fall to his demands, Rumm threatened to shoot the kitten himself. Still uncompliant, Rumm decided not to shoot and left the kitten to die slowly and painfully. Taking more drastic measures, he brought in her father (who had become brain-damaged as a result of Kerrigan's accidentally unleashing her psionic powers) in an adjacent cell to hers and threatened to inject him with the same chemical if she didn't use her psionic powers. When she still refused, threatening to use the power to kill herself and her father, Rumm forced her to be neural resocialized (a form of brainwashing technology used to enforce obedience and shape new memories), turning her into a loyal puppet of the Terran Confederacy. Even after the mind-rape, he continued to mentally torture her for over a year.
Arcturus Mengsk is initially portrayed as a well-meaning freedom fighter against a corrupt government that murdered his entire family before nuking his entire world, and willing to take morally dubious methods to defeat them such as taking their Psychic Beacons and using them against the Confederacy to lure the Zerg to their bases. But when he leads the assault on Tarsonis and uses these same beacons to lure the Zerg to a heavily populated world he shows that he’s more fixated with revenge and personal power, sending Kerrigan down to stop the Protoss from distracting the Zerg from wiping out all of the old families and then abandoning her when the Zerg overwhelm her position, resulting in her transformation into the Queen of Blades. Afterwards he uses the power he has gained as Emperor of the newly established Terran Dominion to oppress any political protesters, continue the Confederacy’s experiments on civilians and orders the death of the last of the old families, a group of teenagers who weren't even aware of what had happened.
The four-part comic Frontline series introduced Dr. Stanley Burgess. A sadistic Terran Dominion scientist, he personally oversaw the neural resocialization of Jin-ho Lim, a terran of Asian ethnicity who opposed the Terran Dominion but was conscripted into the Dominion Marine Corps. After the operation, Stanley ordered the now docile Lim to kill his wife and fellow Terran Dominion opposer, Anna, and he complied by shooting her in the face without a moment's hesitation. He also was responsible for the creation of the terran/Protoss Gestalts by implanting the organs of captured Protoss into terrans controlled by neural conditioning and neural inhibitors. His project came to an end after one of his subjects, Gestalt Zero, was freed from his neural inhibitors by a dying Protoss and stabbed him to death, ironically echoing one his previous comments "I should warn you...this is probably going to hurt."
A relatively minor character in the novel "Devils' Due" is arguably the most irredeemably evil character in the setting, and has no justification in his background. Ezekiel Daun is a bounty hunter and mercenary, and unless his clients specify otherwise he will torture his victims to draw out their death, and makes it theatrical by terrifying them and using psychological warfare before he moves in for the kill. He also records all his deaths as holograms, both to watch in his spare time for the memories and to show his future victims to terrify them even more.
Cliché Storm: The series has always been accused of being this.
Germans Love David Hasselhoff: Competitive StarCraft is absolutely dominated by South Koreans. Of the ten most successful tournament players in the world (as measured in dollars earned via tournament play), only one of them is a "foreigner"—that is, a player who grew up outside Korea. It's something of a Rite of Passage now for a foreign player to defeat a Korean in tournament play.
Goddamned Bats: Early worker units become this, especially Probes, who can warp in buildings anywhere instantly and move on to keep running. Terrans can use ranged Marines to shoot them down, zerg and protoss have melee units, so no such luck with them.
"I'm in ur base, scouting ur tech, disrupting ur mineral line with pylons, stealing ur gas, delaying ur hatchery!"
While Raynor himself is not this trope from a narrative standpoint, he is considered this in-universe by General Horace Warfield:
Warfield: "You magnificent son-of-a-bitch, heheh, you're the last man I expected to see."
A straighter example would be Arcturus Mengsk. By exploiting fear and hatred of the Confederacy he rallies allies to his cause to fight them, building up to ever-more inhumane acts in his war and keeping it from those he knows he can't trust. By the end of a single mission chain, he's shattered the heart of the Confederacy and crowned himself Emperor of the newly formed Dominion, and blames the loss of the Confederacy on the Zerg so most of the remnants of the government will join him willingly out of fear of the Swarm.
Infested Kerrigan. The entirety of Brood War is her going from a Blood Knight to an Evil Overlord, and she does so by manipulating every other faction in the game. By the end of the expansion, all of her enemies are marginalized or dead, and she reigns supreme as Queen of the Zerg. And to boot, she was able to accomplish this because everyone either underestimated her or thought she was reformed. Kerrigan herself notes this to Zeratul:
"[she] made the mistake of underestimating my power, just like everyone else did."
Valerian Mengsk. Though some of it is a result of others, the fact remains he instigated and took part in a grand plan that has currently culminated with Valerian sitting on the Dominion throne, and Raynor and Kerrigan, previously the biggest threats to Arcturus's reign, are his allies, or at least are not his enemies anymore.And it's public knowledge that he did all this as well as helping de-infest Kerrigan, so he's likely going to be hailed as a war hero that brought peace and stability to the sector. He may be a far better man for it, but Valerian is definitely his father's son when it comes to planning and acquiring power.
Kerrigan, when she killed Fenix and Duke after they helped her. And she tortured Zeratul mentally.
Mengsk keeps edging up to it until he finally jumps over it by sacrificing Kerrigan so that the Protoss will be unable to save Tarsonis from the rape of the Swarm. An early draft for the ending to Heart of the Swarm would have Mengsk torture Kerrigan using a device he implies to have had with him even while she worked for him, when telling her that he always considered Kerrigan "an animal". Might very well be true considering how, in novels, Mengsk specifically recruited Kerrigan because she was the assassin who had (while brainwashed) killed his parents, and he had plotted revenge ever since.
Arguably, DuGalle when he sent Duran to kill Stukov. Note that the arguable portion stems from how he was pretty much duped into doing it.
Play the Game, Skip the Story: While the series does have a good sized fandom interested in the plot and characters, that isn't nearly what the games are famous for, that being the multiplayer aspects. The fans interested in the story and the ones that play the games for the multiplayer are worlds apart.
Remember the Mutalisk portrait? Look at the concept arts, and their appearance in SC2. That is not their face. Also take a moment to read about their method of attack. Yup. They are shitting parasites at the enemy.
Upon finding Kerrigan after she's been infested, Raynor is disgusted with himself, as on some level he finds her new form just as alluring as her human form, and maybe more.
Strangled by the Red String: A lot of fans see the love story between Raynor and Kerrigan as this. To be fair, the game focused more on the battles and the strategy, so we have no idea of what happened between them offscreen. StarCraft II makes a much better job at fleshing out their relationship.
As Mike Liberty points out in one of the novels, Raynor is one of very few good and honorable human beings in the sector. And he keeps watching his friends die or betray him, and he gets to live with the knowledge that the evil overlords of two of the factions got there with his help.
There's also the story of his wife and son. Johnny got drafted into and (supposedly) died in the Ghost Program and Liddy died of grief not long after.
Also Kerrigan and her fate in general. She certainly didn't originally plan for infestation.