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.
There is a trend for the characters to fit both their standard interpretation and their Alternate interpretation concurrently, usually changing it up between episodes. This tends to be because the episodes are inconsistently written such that some are very intelligent and sensitive to the issues surrounding sentient life equivalency and the progression of humanity, and some are... not.
Ass Pull: The wormhole drive in the finale. One of the producers commented that its use in the finale was meant to set up the viewers for its use in an upcoming Atlantis movie, meaning that the writing crew tried to pull a Chekhov's Gun out of their ass.
Base Breaker: Rodney McKay. You either like that the smart guy is the one who saves the day or find him incredibly grating. The fact that it is often very easy for one person to be in both camps at the same time makes things... confusing?
Michael Kenmore is a former Wraith who was turned into a human by the Atlantis expedition through a retrovirus cure. After he discovers his true origins, he escapes back to the Wraith and kidnaps Teyla, the sole person who connected with him, to feed on her. He reveals the location of Atlantis to the Wraith but realizes that they will kill him for still being partly human, so he turns to Atlantis to defeat the hive. With the whole hive converted but the Wraith slowly regaining their memories, Michael takes charge of the insurrection and kills another Wraith who might have blown the lid on their plan. Michael escapes, becoming an Evilutionary Biologist who tries to create a perfect race that will be mindlessly obedient only to him and wipe out everything else. He first creates monstrous, Xenomorph-like soldiers by allowing Iratus Bugs to drain human test subjects to death. He later finds a suitable middle stage between humans and Wraith which he dubs Hybrids. He releases a virus on several inhabited worlds that kills most humans and makes the survivors poisonous to all Wraith who feed on them. He creates a clone of a recently deceased Atlantis team member, then tortures and experiments on him for months. He kidnaps Teyla's whole tribe to experiment on them and turn them into Hybrids, including her boyfriend Kanaan. He kidnaps a pregnant Teyla to harvest her baby's unique DNA for his Hybrid project and plans to kill her after delivery. Finally, he briefly takes over Atlantis itself, where he tries to kidnap Teyla and her baby again and blow up everyone else on the base out of spite. When the pair escape, he decides to leave them to their deaths as well before attempting to decapitate an unconscious Ronon to take his head as a trophy.
The Wraith "King" or "General" from season 3's "Sateda" is one of the worst Wraith lords that Atlantis has ever encountered. He's a sadisticBlood Knight who commands one of the strongest Hiveships in the Pegasus Galaxy and terrorized their sector even while the rest of the Wraith were hibernating. His unprecedented rule over a Hiveship, which among Wraith derive their legitimacy from being ruled by a Queen, confirms him as a tyrant or even of having murdered his Queen to usurp her place, an extreme taboo among Wraith. Having already participated in the harvest of dozens of planets for centuries, he destroyed Ronon's homeworld Sateda, annihilating the entire population. Ronon's wife was killed in front of him when the Wraith started bombarding Sateda's hospitals. He made Ronon a "Runner", implanting him with a tracking device so his soldiers could hunt Ronon from planet to planet for sport, wiping out any human settlements that offer Ronon shelter as well. He promises the survivors of one such settlement that if they capture and return Ronon to him, he'll leave their planet alone forever. They do so years later, but he harvests them all anyway. He returns Ronon to Sateda specifically to watch him die there, boasts how many of his fellow Satedans he devoured, and organizes a hunt for Ronon by sending in increasingly bigger groups of Wraith hunters while watching the show from his ship. When this fails, he tries to beat Ronon to death himself and feed on him.
Crowning Moment of Funny: Doctor Zelenka returning from the planet of the children in "Critical Mass", and Rodney commenting "Mister Mom...fun with the kids?" (He's covered in facepaint and has straws woven into his hair) Zelenka turns to him and says: "Do not even speak to me!"
Designated Hero: Although our heroes are in general good guys who try to do the right thing, there are quite a few times where what they do is at the least soaked in Moral Dissonance and at the most downright evil. They have an incredibly warped perspective about sentient life such that only human and human-like beings matter and are disturbingly willing to exploit, manipulate, experiment on, mass murder (as in killing huge numbers in cold blood) and double-cross anyone or anything that poses a threat or can be labelled an enemy species, even treating one of their own expedition similarly when they come back as a replicator.
In "Infection" where Sheppard comes across 'Todd's completely defenceless diseased Wraith hive ship where his entire crew - now having undergone a gene therapy where they can no longer feed - are in stasis pods. Originally the plan was to just leave them or blow up the ship, However, because of the ship's malfunctions there is an off-chance that they might break free from the pods. Sheppard's solution? Suffocate the hundreds of Wraith in their pods and use c4 to blow up any pods that are unresponsive to the "suffocate their occupants" command. The Team decided that if the gene therapy really was effective at killing Wraith, they should try to disseminate it to as many Wraith as possible for use as a biological weapon.
Designated Villain: Bates, Kavanaugh and Ellis tend to end up in this role. They usually have legitimate concerns or complaints, but because these are against the main cast of characters and expressed in a way that is distinctly in favour of their own self-interest (Bates seeing Teyla as a security risk and willing to essentially exile her people to protect the expedition members; Kavanaugh complaining to Weir about Weir dismissing his concerns or dressing him down in front of his team when he priorities a course of action that puts the safety of Atlantis first no matter the risk assessment or loss of life; Ellis undercutting Weir's authority behind her back because she challenges his opinion and his own authority, and wanting McKay to cut the exposition and get to the point in a way that pointedly bullies and demeans him) the characters are presented as reactionary jerkasses. There is also a trend of portraying Kavanaugh, in his few appearances, as a coward even though every time he is up against a situation in which his fear is perfectly understandable, although he does consistently advocate a course of action that will save himself and whoever is with him while sacrificing other people, sometimes even when the risk to himself is minimal.
Ellis isn't so much a Designated Villain as a Jerk Ass who likes to bully and harass those who make him feel inferior. He's a good man, a competent officer (as befitting his rank), and takes pride in making the right call, but doesn't like it when people who are smarter than him have an idea or explanation that he finds difficult to grasp. Both times he doesn't tell McKay to cut the exposition and get to the point, he insults and harasses him for giving a long explanation, often one that is necessary to understand what he's trying to tell him. The first time, he cut him off and then McKay had to go back and explain the entire thing all over again because he didn't understand. The second time he outright bullies and degrades Rodney in a meeting so severely that Samantha Carter has to tell him that if he ever talks like that to someone again she'll have him forced off Atlantis. And that's really saying something (I.e. Sam wouldn't defend Rodney like that unless what Ellis was saying was absolutely unacceptable, particularly considering that he's of equal rank)..
Michael is a subject of some contention with this trope. Many people express their disapproval of how Michael is treated, and/or focus more on the terrible way he was turned into a villain rather than the aftermath. As such, it is easy to presume that all this "Kill almost everybody and turn the rest into an unstoppable army of destruction" thing kinda slips their minds and Michael gets the Draco in Leather Pants treatment by default. That said, disapproval of his treatment doesn't mean approval of his actions - and just because the enemy is evil, it doesn't mean the heroes get a free pass to go play at the Moral Event Horizon. In a very straight use of this trope, though, some people do in fact sympathize entirely with Michael and do in fact forget that he ended up as an Omnicidal Maniac who would use a baby to perfect his mindless army, no matter what made him that way.
You wouldn't believe how many fangirls Todd has. Although Todd, despite being a Manipulative Bastard, has saved Atlantis' hide a number of times and has never tried to destroy them (despite multiple opportunities) or use what he has gained from them against them (except for the Otterus device incident). Although self-serving and human-eating, you. really can't classify Todd as a villain all that much, let alone one of Michael's Omnicidal Maniac caliber.
Engaging Chevrons: Played straight and subverted in "Rising". A big deal is made out of dialing the 8th chevron to actually get to Atlantis. Later, McKay slips into Walter's old "Chevron One... Encoded" routine the first time the Atlantis gate is dialed and gets a dirty look from Weir. After that it's never done again, since the Atlantis gate can be dialed in a matter of seconds.
Also Major Lorne and the gateroom tech. Fandom assigned first names to both of them (Evan or Nick — usually the former — for Lorne and Chuck Campbell for the tech), and the latter became a case of Ascended Fanon.
Todd the Wraith.
Fan-Preferred Couple: Depending on the fans preference for gay or straight couples; John/Rodney and John/Elizabeth. The former has a count of 2,516 entries on fanfiction and the latter 2,364. In comparision John/Teyla only has 1,184.
Fridge Horror: Sheppard's story in 'Remnants' when the characters control their own hallucinations. While Woolsey and Rodney create innocent and even happy visions of love interests and friends, Sheppard hallucinates Koyla taunting, beating and torturing him for hours on end. (Including cutting off his hand). And when he realizes it's not real? Turns out that he believes he deserves to suffer for everything he's done wrong. Worryingly, the series never returns to this so presumably Sheppard ended the series still drowning in self-loathing and emotionally torturing himself. (Made worse as all his friends have paired off and are living their Happily Ever After).
Genius Bonus: Genii is the plural form the Latin word "Genius" (no pun intended).
Growing the Beard: All the Badass characters either show up or are promoted in season 2: Ronon, Caldwell, Lorne, Sheppard, etc.
Sheppard and McKay are everyone's favorites with scenes that seems to back it up (the end of Irresistible for expamle).
Beckett and McKay are great friends and even kissed once while McKay was sharing a body with the mind of a female soldier.
A Foe Yay example is the relationship between John and Todd (the Wraith), especially when they formed the first human/Wraith alliance to escape a prison together. Though they're basically enemies and don't trust each other, they're friendly enough to work together in several episodes.
Ho Yay Shipping: Most notably, John Sheppard and Rodney McKay. There are some people who watch the show specifically because of this.
The whole Series Finale, with idiot plotholes, stupid character decisions and Ass Pulls all around. To give an idea of the problems in just one aspect of the finale: bringing Sheppard to Earth and not putting him in the chair but letting him pilot a 302 instead because...? Putting the chair not half a mile under what amounts to an icy fortress with one entrance (Antarctica), or a similar easily defendable structure, but in an easily targeted warehouse with no air defence because....? The stupidity of defending the entire earth with a handful of 302s because....?
One thing that becomes really frustrating is that a number of simple solutions to any one of a number of situations present themselves, and the characters steadfastly ignore them with not even so much as a Hand Wave to explain why.. For example, when Atlantis finds that upon dialling Earth, the wormhole opens in the modified hive ship, which has a gate inside it, why they don't simply overload one (or even two) of a number of Atlantis's now surplus naquada reactors and throw it through the wormhole to blow up the hive ship is because....? They could have thrown through any number of explosives, over-loaded reactors, energy weapons, shot drones from a puddle jumper, or even overloaded the gate, but they send through one team of people instead.... What.
The entire retrovirus subplot in Season 2 & 3. First strike for carelessly leaving the unfinished formula out in the open for a scared little girl desperate for a cure to get ahold of. Then their experiment on a captured enemy Wraith backfires spectacularly and blows the expedition's cover. Then when aforementioned Wraith seems to put the incident behind him and offers himself as a potential ally, the team betrays him again. Unsurprisingly, it backfires just as badly as the first time, and they lose their own Hive ship for the effort.
S01E05, Suspicion: After the team is attacked very early on during numerous excursions by an alien civilization whose biological, technological and/or tactical, strategic, and intellectual capabilities are for all practical purposes completely unknown save for the very barest of details previously obtained from rare surviving eyewitnesses, the only viable explanation for the problem is apparently that someone high ranking among their close allies, who are themselves prey for the enemy and literally require them to help ensure their survival, must be a traitor.
5.14 "Prodigal": Michael and his Hybrids are suddenly afflicted with Idiot Balls in their final appearance to make the All Your Base Are Belong to Us plot last long enough, because Michael technically already wins in the opening. This overlaps with a Villain Ball because Michael stretches out their take-over specifically so he can activate the self-destruct. The mistakes they make are still legion:
Not leaving Teyla unconscious until they're clear of Atlantis by stunning her repeatedly or even restraining her while she's awake so she can't, say, take her mission-critical baby and flee from your grasp at the first opportunity. This can initially be explained by Michael wanting to offer her to join him willingly, but when she refuses, he has no excuse for even risking it.
Leaving all the gate room people, two dozen or so stunned humans (including The Big Guy Ronon), in an unmonitored room with an accessible door panel and a single guard posted at the other side of the door. The Hybrids could have just killed them all to save themselves the trouble of bothering to seclude them after they've been knocked unconscious. They were already planning on blowing up Atlantis anyway, so they had no believable reason to keep them alive beyond plot-required stupidity.
The Asurans. The Lanteans tried to wipe them out, and the Atlantis Expedition later tries exactly the same because they're dangerous. Its even noted at one point that the reason they're envious of Humanity is because they see us as the favourite son who recieved all father's attention.
Of course, the "jerkass" part comes into play because their plan to destroy the Wraith was to wipe out their food source; in other words, every single human in the Pegasus Galaxy.
But this only happened because instead of rejoicing in creating artificial intelligence so advanced that it developed consciousness and compassion, and taking out the aggressive programming that made them a threat, the Altarens decided that they were Not Even Human and just wiped them out. After being treated like that its no wonder they are so distanced from biological intelligence: the only ones they knew were Abusive Parents.
The engineer in "The Ark" who was awakened to find that his family did not survive. He's completely distraught, and you sympathize with him. When he kills himself by burning himself up in the engines of the shuttle that was supposed to transport the last of his people, it's a little self-centered but still understandable... until you find out that he was trying to vent the entire moon station that he, his people, and the team were on into space via explosive decompression, using up all the fuel needed for the shuttle in the process of trying to kill himself and everyone else, and that in order to save these one thousand people he was complicit in the murder of hundreds of thousands who were slaughtered by atomic radiation in an Extinction Level Event that his people enacted so the project would succeed. Keeping in mind that this is the very last of his entire planet, and that the thousand left include two hundred children.
The Wraith "Todd" lives this as a matter of course; manipulating enemies with style is like breathing to him.
Major Sheppard also gets a moment like this every so often, including and especially at the end of the series, when he's trying to talk "Todd" into helping them fight another Wraith. "Todd" asks Sheppard why he should do it when it would leave "Todd" the prisoner of Atlantis and without any leverage.
Todd: Am I supposed to be enticed by this offer?
Sheppard: No. I'll probably kill you anyway. But don't forget, this Wraith betrayed you and got away with it. For no other reason, you might want to do it out of pure spite.
Todd: Youuuu know how to talk to me, John Sheppard! (evil laughter)
Kolya's feeding Sheppard to "Todd" the Wraith is seen as this by everyone, including Kolya himself.
McKay: Kolya! He could have left you to die! He does not deserve this!
Kolya: Let's be clear, Doctor McKay: no one does.
Turning Michael into a human for the second time, after he's not only sacrificed his own kind but helped the Atlanteans out multiple times, counts as this for some. The fact that the humans don't even think they're doing anything substantially wrong is what makes this even more horrifying.
Killing the Asurans comes close to crossing the horizon.
What Atlantis does to the Asurans who only wanted to Ascend - condemning them to an And I Must Scream fate - goes right over the horizon and keeps on going. Weir in particular stands out, as she was the leader of the group of Asurans and the betrayal is revealed to have been her plan, hence why went through the Gate first to convince them it was "safe" on the other side.
The Ancients attempt to wipe out the Asurans is equally horrifying. When we wished that the Ancients would have cleaned up after some of their messes, we didn't mean through carpet-bombing!
The hallucinations in the season 1 episode "Hot Zone", caused by an Ancient nano-virus.
In "Doppleganger", the malevolent crystal entity that assumes Sheppard's form in people's nightmares, is capable of scaring people to death such as Kate Heightmeyer and provides no real reason for it's actions other than It Amused Me. When it's returned to it's homeworld at the end of the episode, we see that there are hundreds more of these crystals stretching for miles around.
Shipping: A lot of it, with Teyla/Kanaan, Ronon/Amelia and McKay×Keller all now canon. (Although most fans were not happy about the last one).
As indicated above, the largest slash ship in the fandom is John Sheppard/Rodney McKay, although there is a decent portion that also enjoy seeing John/Ronon and Ronon/Rodney.
John/Elizabeth and John/Teyla were both Ship Teased. He has kissed both women at different times and have share quiet moments with them, but usually through some sort of plot device instead of actual romantic feelings. The Legacy series of spin-off novels still enjoy teasing the John/Teyla angle, but the novels' canonicity is dubious.
The John/Teyla ship was also neglected in later series as Ronon/Teyla was introduced and Kanaan/Teyla became canon. However the most popular straight pairing is still John/Elizabeth, especially as John remained single after her death (her death itself caused outrage among the fans).
The writers also Ship Teased Ronon/Keller before deciding to go the McKay/Keller route, which the fandom reacted much more positively to (it didn't interfere with shipping McKay/Sheppard, and Ronon was pretty popular so fans liked the idea of him getting to be with someone).
Michael points out the considering the Atlantis expedition's treatment of not only him but anything that isn't human or is a threat, they are incredibly similar to the Wraith. The fact is, he's right. If the Atlantis expedition had been the bad guys, their behavior would have put them beyond the Moral Event Horizon.
However, John's 'alliance' with Todd went a long way to helping to get back to moral ground, showing that yes, Michael was right, but being incredibly similar to the Wraith isn't always a bad thing. Remember, the only thing the Wraith can feed on is humans. They aren't the Goa'uld.
Furthermore, as several Wraith characters point out, it's not as if they have a choice in feeding. While they do possess a digestive tract and are capable of eating regular food, they lose the ability to gain any nutrients or sustenance from it during adolescence, when their need to feed on humans first manifests. Ultimately, the Wraith are just as much victims of their own biology, as the humans they prey upon, although their culture which celebrates the feeding process is something we could have definitely gone without.
Unfortunate Implications: Lucius Lavin in "Irresistible" essentially roofied an entire village and Atlantis into being his adoring public, date-raped numerous women and is not punished in the slightest for his actions. Instead, it's Played for Laughs. He gets sent back to the planet after the people are immune to his charms. The implication is that he'll be plenty punished by the outraged villagers he manipulated. Not that this excuses comedy rape. We do find out later in "Irresponsible" that his wives divorced him and he was banished from the village, but even so, he seems to have been let off the hook rather easily. Furthermore, he doesn't appear to have learned a thing about why it's wrong to manipulate people, since he's right back at it in the latter episode!
Villain Decay: The Wraith seem to go through this, especially in the last couple of seasons, due to both Lowered Monster Difficulty and the story changing the emphasis from "the Wraith slowly wiping out all Pegasus humans" to battles against Eviler than Thou enemies such as the Replicators and Michael. Todd also helped with the Villain Decay, because he gave a lot of insight into Wraith culture, and someone decided not to make them as evil as we were first led to believe.
Visual Effects of Awesome: Considering the typical production values of an average sci-fi TV series, the series has amazing CGI effects. Most prominent in "The Siege" three-parter episode.
The Woobie: Poor, poor Michael... at least in his first episode. After a while he's just a Jerkass. Well, after the second time Atlantis has betrayed him and tried to kill him.