The NerveGear has medicinal value for the terminally ill—it can slow the progress of some diseases by conserving energy, and they can experience things in the game that their illness prevents them from doing in real life. This is actually a key plot point in Book 7 of the light novels, as Yuuki and the other Sleeping Knights are all hospitalized for various reasons—Yuuki is terminally ill with AIDS, for instance.
According to the novels, Asuna never had an interest in food in real life. So why did she become a master chef? Possibly because of the simple gesture of Kirito giving her cream for her bread.
Not only that, but she's grown up having food prepared for her; in Aincrad, she's preparing her own food. And as everyone who has ever cooked knows, there's a differences in satisfaction in eating something someone has made for you, and something you've made with your own hands.
There is a brief mention in the first volume about cooking in Aincrad not being as fun as real life, suggesting she might have cooked some in the real world. Considering the fact she does so at the end of the Fairy Dance arc this isn't impossible. This means there is another reason behind her mastering that skill; it was something familiar to her.
Alternatively she took up the skill because she wanted to find something she could relate to from the real world. Going off of the above, then naturally cooking would work for her.
As a genre-savvy young girl, Asuna also knows the best way to get her guy is Through His Stomach, and Asuna brings up her newfound skills wherever Kirito is around, offering to cook his rare Ragout Rabbit and insisting to share her food with him wherever they're in mission. Since Kirito had shown her some kindness, she was trying her hardest to impress him.
The whole incident with the 75th Floor Boss is a deliberate echo of the Black Cats of the Full Moon, with Asuna representing all of Kirito's comrades. Which is why Kirito loses his fighting spirit when he sees Asuna struck down. He loves her more than anything in either world, and the thing he most wanted to make sure never happened again happened again right in front of him, and again he was unable to do anything about it.
Why is it that SAO lacks a traditional Magic system, unlike other Role Playing Games? Because Kayaba wanted to keep this game as relatively close to real life as possible! It'd be hard to forget you're in a game when people are hurling lightning bolts at each other!
Since SAO lacked any sort of government, Kirito decided to become Sheriff. That's why he's called upon to investigate murders. On that note, Sword Art Online invokes a Western trope of the sheriff confronting the corrupt mayor. Not just western: basically Kirito acts like the lone samurai of your average jidai-geki: cue to Mito Komon, where the dismissive, non-confrontational nice guy just tags along to witness something evil and then, after a Badass Boast he opens a can of whoop-ass on the bad guys.
Yui looks quite a bit like what you'd expect a biological daughter of Kirito and Asuna to look like: She has Asuna's features, but Kirito's hair and skin tone. The Fridge sets in when you realize she must have based her appearance on them when she wanted to meet them.
It's shown that Kirito has more sympathy for Kayaba than for Sugou, even though Kayaba harmed more people than Sugou did. The reason behind this is because Kayaba truly loved SAO and the VMMORPG genre and, while he indeed killed more than 4000 people, it was a restricted case. Sugou, on the other hand, only saw ALO as a tool for his ambitions and vain glory.
Additionally Sugou used his authority to rule as a king. He installed himself as "High King" of a virtual world, and treated everyone else as beneath him, and made an actual in game quest that's supposed to let players ascend the World Tree to have an audience with him and made an "Alf" impossible to complete. Kayaba actually made his game winnable and actually assisted the players by joining them on the front lines in disguise.
After escaping SAO, Kirito is shown going toe-to-toe with his sister while still using his movements from the videogame. Yes, he was comatose for 2 years, but Damn You, Muscle Memory! still applied to the brain, so the motions were ingrained that way.
The second arc, particularly in the anime due to it being a more visual medium, has a huge spike in fanservice, with Gainaxing and Chainmail Bikini armour everywhere. In ALO, everything is run by Sugou, the creepy misogynist who sniffs comatose girls' hair. The fanservice spike is because he designed the game that way.
There's also the fact that, barring the matter with Asuna and the other 300-ish SAO survivors, Alfheim has much less at stake than Aincrad did.
Leafa's reaction to Recon's Love Confession probably had something to do with the fact that he sounded like he was asking her to marry him out of the blue.
Much flak is given to Asuna for being a Distressed Damsel, and not even trying to escape. But consider her situation: Stuck in ALO by Sugou, who has full GM privileges, and he is not one to disregard advantages. So she's forced into a revealing costume, placed into a cage that she cannot break/affect ('immortal object' by all rights), and literally has a blur over her vision whenever the exit code is inputted, though not when viewed through a mirror; that we know for certain. Considering Sugou's personality, he has also most likely placed a barrier around the cage, to prevent her from slipping through the bars - or alternatively, even if she did, falling down and dying might just respawn her back in the cage. And would even he allow her to keep her ALO skills and abilities to ambush him? Simply put, there really was little she could do, and she clearly hated this... but she held out anyway, and nearly got out despite all this.
On the first day of SAO, Kirito refused to escort all of Klein's friends, for fear that he wouldn't be able to protect all of them, and figuring that he would blame himself if any of them died. Thing is, this is a flashback being narrated by Kirito after the 74th floor has been opened. Is Kirito recalling his actual feelings from that day, or is he projecting his memories of the Black Cats of the Full Moon onto his memories of that day?
In Episode 19 of the anime, when Kirito and Leafa are fighting the Salamanders who had tracked them, pay special attention to what Kirito does after he uses his illusion magic, and it becomes clear why he picked The Gleam Eyes as inspiration for it: he's making the Salamanders feel exactly what the Liberation Army felt in the Floor 74 boss room.
Big frickin' monster that towers over everything they've fought so far (to our knowledge): scare them off the start, make them realize what they've gotten into - which the Army felt when Corvatz made them march into the boss room half-cocked
Killing their shield users first: give them the horrifying realization that they don't stand a chance - which the Army would have realized when The Gleam Eyes caused their first casualty
Leaping in front of the retreating spellcasters: let them know that they've walked into this and there's no getting out - which the Army knew when their teleportation crystals failed to activate
And finally, letting the last guy live (albeit at Leafa's request): making sure they know that they tried something stupid and should not do anything like that again - which the Army knew when Kirito and Asuna saved their asses.
In the "Alfheim" arc, Kayaba returning Back from the Dead to grant Kirito his admin account and powers and the World Seed may seem a cheap way to give closure to the plot. But actually, from Kayaba's perspective was the best thing to do. Despite being clearly victimized by Kayaba, Kirito still tried his best to enjoy and protect Aincrad, his finest creation. On the other hand Sugou, motivated only by greed, his delusions of adequacy towards Kayaba and his vilest instincts acquired Kayaba's patents just to squander them into a pale, vile imitation of his dream and weaponize his research. Basically, Kayaba used Kirito as his physical proxy and champion to wrest his uncorrupted dream from the hands of a thief. Kirito in the anime pretty much sums that up, claiming in his Badass Boast that, while both him and Sugou suffered at Kayaba's hands, Kirito was forged into the Hero of Aincrad and Sugou became a petty, green-eyed crook.
During the opening credits for the "Gun Gale Online" arc, Kirito can be seen writhing behind Death Gun while surrounded being circled by three shadows. This could be foreshadowing that Death Gun is actually three people.
It's could also represent the three Laughing Coffin members that he killed.
Something that may be obvious to some, but others might've not realized it, when Heathcliff kills Asuna, her sword is left on the ground and Kirito picks it up to use, people might wonder why it didn't disappear since she was dead, but Kirito and Asuna were married and shared an inventory, so Lambent light would've instantly become Kirito's the moment she died.
Speaking of the above, Heathcliff killing Asuna, incident, in Red-Nosed Reindeer, Kirito gains an item that allows you to revive a player within a short, limited amount of time. Meaning it's not surprising that Heathcliff, as the GMPP, was able to allow both Kirito and Asuna to live once Kirito beat him.
Alternatively: Said item lets you revive a character shortly after death, but before their player dies. That means that, as long as that item exist, their is a small time frame between character death and player death... and it might have been easier to program it to always have that gap, rather then check for whether it exists. If both Asuna and Kirito died, but the game was cleared during that gap period, then they both lived because by the time the killing function would have activated, said subroutine was deleted, and so couldn't fire.
Why does Kirito hurry to Sinon's apartment even though she told him not to? Because of the Black Cats of the Full Moon. He learned from that incident to always err on the side of caution. No sense taking the chance that the murderer might still be there or set her apartment on fire or something like that.
Everyone referring to Freyja as a trap during Calibur. She is, in the slang sense.
The only girls in the crew that Yui tolerates besides Asuna are Leafa and Sinon. Why? Because Leafa is family and Yui can sense that Sinon doesn't have any romantic feelings for Kirito, but she can sense that the others do.
Why is Kirito able to pull off a convincing feminine act in GGO? Appearance aside, he copied the gestures and body language cues of Asuna and the politeness of Yui to make the act more convincing.
He was also has a sister and a Aunt who he's lived with for his entire life. More chances for him to know how to act feminine.
Kirito was blamed by Keita for the death of his guild the Moonlit Black Cats, because (according to Keita), Kirito hid his true level from the rest of the guild. However, that doesn't make sense because...In Pokemon, whenever you have a Pokemon that is at least 10 to 20 levels higher than anything else in your party that Pokemon becomes a Crutch Character. You take extreme challenges because you "know" that the super-strong character will always be there in the nick of time to save you and the rest of your team. That's all fine and good, except that the game was designed to kill the player shortly after the character dies. If the rest of the guild had known Kirito's true level/power/strength then it's almost assuredly likely that they would have rushed into the trap sooner, therefore being killed sooner. In fact, given Asuna's actions in the "Mother Rosario" arc, one can't help but realize that Kirito had a point doing what he did. Asuna showed the Sleeping Knights (who were already super-powerful compared to other players) even a fraction of her true power, and they did a 7-person boss-rush. And failed. Would the Black Cats have done much differently than the Sleeping Knights?
Unless the trap was leveled. In that case, the fact that Kirito was at a much higher level then the rest of the Black Cats would have screwed up the calculations, thus making the monsters spawned by the trap much more powerful than they would have been if Kirito wasn't there. If that's the case then it really is Kirito's fault that his team was killed.
There are a few moments in Aincrad where it's described that Kirito or Asuna are doing things that shouldn't be possible in the system of Sword Art Online. There is some speculation of Maybe Magic, Maybe Mundane, but in reality it is simply a function of the Nerve Gear, albeit an unsuspected one. In times of great worry or duress, it's been shown the human body can do things far beyond normal physiological limits. Since the Nerve Gear works by intercepting signals meant for the body and transfers them to the avatar, it only makes sense that these "override" mental signals would transfer as well.
A fun one in Sword Art Online: Hollow Fragment concerns Sinon's weapon. At first, she can only use basic daggers, and she is therefore a relatively weak character, because she's a ranged fighter... then, presumably, the World Seed for Aincrad creates a quest to earn a bow, Sinon's signature weapon...
Another one from Sword Art Online: Hollow Fragment in relation to why Strea looks older than Yui and the seven other Mental Health Counseling Programs despite being the second one made. It's because the character data she merged with. Strea either took on the appearance set within the data, or adapted to it which caused her original body to change and match the age set in said data. Because she's an AI, she may not be aware her programming's been changed.
Her personality could have also been effected by the same data which explains her Innocently Insensitive nature, because while her body is that of a teenager or adult's, her mentality is still that of a child's, so she doesn't have the knowledge to fully understand what she's doing, and just like with her appearance she's unaware her programming's been changed.
Why do the other characters not consider this when Yui mentions the unused character data to them? Because they never met Strea before this and wouldn't know of the change, while Yui was unaware for most of the game that Strea was an AI like her.
How is it that Kirito is able to beat Yuuki in Hollow Fragment when in canon both Kirito and Word of God state otherwise? Well Lost Song features the Mother's Rosario arc as an in-game event line, heavily implying the Svart Alfheim update was likely added during the Winter during or right after everyone escaped SAO. This means everyone was trapped in SAO for three years in the game continuity, the same amount of time Yuuki's been in a FullDive for. In other words... Kirito was able to win against Yuuki because they had both lived in the virtual world for three years straight, allowing him to grow much stronger than in canon, making them equals in the game continuity.
Further proof to how this one year made him a stronger player shows in Kirito's duel with Sumeragi, where he manages to chain 5 sword skills with the Skill Connect ability. He says he's usually lucky to manage 3 or 4 in a row in the main continuity.
A minor one in the games. In Sword Art Online: Lost Song, Kirito is able to detect a player named Rain following him and his party on more than one occasion. Granted, we know that Kirito's detection skills and reflexes are top-notch, but it's possible that he knows how to detect players following him because he's familiar with this kind of situation. After all, Kirito had plenty of hide-and-seek practice with Strea back in SAO (in the past SAO games). In fact, one could say that his detection skills increased in that time frame, and since stats carry over from SAO to ALO, Kirito's heightened detection skill was also brought over, which leads him to be able to notice Rain because her hiding ability is lower than his detecting ability.
Another minor one from Lost Song, in the American version Seven's real life name being changed to Rainbow has even more meaning than her original name when you remember that Rain's real name, Nijika, is japanese for rainbow. Where does each sister live again? America and Japan, they're names are the same word in their respective countries.
"That's not possible!" said three or four times should give you a clue that we don't know something, especially if Kayaba says it about anything anyone does inside SAO. Then we learn about Fluctlight...
Kirito fought a duel against Asuna to dissuade her from going through with her plan to lure out the boss into a village and defeat it while it's busy killing NPCs, because that would be cruel. The Fridge Horror is that based on everything we know about bosses and NPCs in Sword Art Online, that plan had no chance of working. If they had gone through with that plan, it is likely that it would have gone horribly wrong. If Kirito hadn't been so protective of the NPCs, a bunch of raid members might have died attempting an impossible strategy.
At one point when Kirito is lost in thought in SAO, he's casually asked if he's lagging. Wait, this game still has lag?! That is...not acceptable! Even if you're going to throw people into a video games that kills them, you should at least feel obligated to make sure people don't die because they have bad wifi.
There's only ONE person in all of Alfheim Online who could get into Sugou's special area, who wasn't already there, and 'beat' the quest... and it's NOT Kirito. Due to the access lock-out on the entrance, if Kirito hadn't loaded Yui into his ALO account, he'd have wasted all that effort, since as mentioned above, he only became Alfheim's superuser AFTER the door was opened!
After the arrest of two of the Death Gun conspirators, Kikuoka says that he expects them to get off on an insanity defense. Thing is, what they were demonstrating was not criminal insanity, but rather classic Serial Killer behavior, having complete control of their faculties right up until their plans fell apart AFTER killing four people. This means that a couple of serial killers are probably going to be released in a few years after being "cured" because they were never insane in the first place. It seems the Japanese justice system needs to buy a clue: trapping 10,000 people in your death game so you can play God without any appreciation for the lives of the people you trapped is criminally insane; making a game out of killing people when you know exactly what you're doing and you're just angry at the world is not insane, but rather typical serial killer behavior.
In retrospect, it's probably a good thing that Kayaba's ex-girlfriend decided not to kill him when she had the chance. See, there's no guarantee that killing Kayaba wouldn't have made SAO unwinnable, since that would have killed the final boss without defeating him in battle. If she had killed him, there's a distinct possibility it would have trapped all the players in the game forever.
Kyouji probably would have gotten away with it if he hadn't had that creepy look on his face. He had an alibi when Death Gun appeared in the BOB preliminaries, as he was logged into GGO as Spiegel, and both Kirito and Shino had seen him there. The only potential witness against him would be his brother, who would not be credible in the face of witnesses giving him an alibi. When Kirito and/or the police showed up at Shino's apartment, Kyouji could claim to have fought off the Death Gun accomplice himself and pin everything on Johnny Black. Had he not had that creepy look on his face, it's likely that Shino would have accepted his proposal, and it's not like he was going to rape her on account of not agreeing to have sex with him then and there.
What was going on in the Shinkawa family that they managed to raise two serial killers? You'd think a doctor with his own hospital would have noticed something and intervened before the Death Gun incident.
Possibly a convenience, but the player's choice of the name "Spiegel" in GGO becomes one if you forget that it's a German word and instead think he's paying homage to Spike Spiegel. You know, the guy who, during one of the show's Signature Scenes points a finger at someone and says "bang"? Kind of makes you think he picked that name just to trigger Sinon.
In Volume 7, Asuna's mother, impatient with her daughter being slightly late for dinner and not knowing that she's logging off, pulls the plug on her Amusphere. It's quite possible that she might have done that back in the Aincrad arc, before word circulated about how forcibly unplugging the NerveGear killed the players, and if she had, Asuna would have become just another day one casualty and the story would have turned out very differently.
The Sister's Prayer side story brings up a scary thought when you remember Yuuki's status as Ill Girl fighting AIDS, Merida was a terminal care patient who would have been one of the 10,000 players trapped if not for her brain tumor before the official launch. Imagine if during the two years SAO was running, other players gained similar conditions or got them shortly after it began. How many of the 4000 casualties of SAO died due to real life illness rather than in-game death?