In the first movie, Winston says: "You dip so much as a pinky back into this pond you may as well find something reaches out to drag you back into its depths." This is the exact description of what happens in this film, as after a brief brush with Iosef and Viggo, something (Santino) reaches out and drags John back into the Assassin depths (the High Table conspiracies).
Was this a simple warning Winston was giving John, or was he trying to remind John that he still had an unfulfilled marker?
Charon is (presumably) named after the ferryman of Greek myth who carries those who pass away to the world of the dead. Besides the obvious connotation with the deadly underworld of the Wickverse, the second movie shows the parallel as more literal: Near the end, it is shown Charon personally drives Wick to the spot where he'll be executed, just like the mythical Charon would.
This also ties back into the first film. Perkins receives a call from Charon to meet with Winston at Central Park. Charon not only delivered John to Winston, he also delivered Perkins. The exquisite irony is that John and Winston meet only a few days later just a few feet away from where Perkins died for breaking the same rules.
Gianna's death seems built to mirror in some forms The Death of Marat, both the painting and the actual event: A powerful political figure is cornered by an assassin and dies. Said political figure's death is the spark that lights the fuse that leads to a massive, insane political upheaval, befitting the implication that there's a war between the High Table and the Bowery King. And while Marat was assassinated and Gianna technically committed suicide, the famous painting evokes the sense of suicide.
The use of outdated technology by the criminal underworld makes a lot of sense when you consider the security it provides. For example, paper records are much more difficult to copy and smuggle out than computer files, and smartphones that are always online provide a clear opening for a security breach. Plus, even if it's harder to have back up in case of a fire hazard or more prone to error than more modern systems, it's not like evidence of your crimes being gone is a bad thing.
The introduction of the old-fashioned criminal switchboard is awesome, but why wasn't it shown in the first movie when Viggo sets the bounty on John? There's the obvious Doylist explanation of they hadn't thought it up yet, but there's a Watsonian explanation, too: Viggo was willing to pay double for anyone who breaks Continental rules to kill John. It makes perfect sense that he wouldn't want to alert the people in charge of the very ruleset he's explicitly telling people he wants broken.
Winston's insistence on rigid adherence to the code of the Continental makes a lot more sense when you realize he's almost certainly the one who laid it down, between his accounts payable number simply being a string of 1s and his checking over the coins early in the film. He probably got everyone to agree to follow those rules to prevent things from simply becoming open war, and he's got no interest in going back to those days. It's why he looks heartbroken when John shoots Santino in the Continental.
John going to the tailor as part of his Lock-and-Load Montage looks cool and lets him upgrade his protective gear, but it also makes sense considering every suit he was shown wearing in the previous film got shot, stabbed, or soaked in someone else's blood.
When the bounty is first introduced, we see multiple people checking their phones to see what the bounty is. Now, pay attention to who we get: a violinist who is a busker, a fat sumo wrestler type, two normal-looking Asian guys, and a pair of janitors. These aren't high-class assassins like John. These are the new guard or the lower levels: basic contractors who happen to be in the system. Yet there are probably more people that got the bounty than these. Why don't we see a sniper on the level of Marcus trying to kill John? Because the high-level assassins know not to mess with John Wick. Ms. Perkins, one of the relatively new assassins, seemed to think she was hot enough stuff to take on not only John, but the Continental, and clearly failed. John's reputation precedes him, so only the people that haven't heard of the full story, or simply think because he's retired, he'd be easy, are going after John. Also, more experienced assassins might have the financial security to not need to take such a risky bounty, whereas the assassins lower down on the ladder are more likely to be enticed by the idea of such a big payday.
Speaking of the sumo, why don't John's groin attacks work on him? Because sumo wrestlers are trained to push their testicles back into their inguinal sacks to prevent injury.
In a clever bit of foreshadowing, when Winston is having Santino declare the Marker fulfilled and is warning him that John will come after him he cryptically asks an uncaring Santino what John will do now that he's free of the Marker. Winston knows exactly what John is capable of as well as John's Fatal Flaw of being unable to let something go. He expected even at that point that not even seeking indefinite refuge in the Continental would protect him from John's wrath. It explains Winston's oddly resigned look despite his apprehension when John confronts Santino in the Continental at the end; despite his urging John to walk away he knew John would willingly take on the effective death sentence of killing on Continental grounds.
Just before initiating their close-quarters fight scene, Cassian repeatedly tries to shoot John, while the latter simply disarms the former by swatting away the gun in an arm-lock. This actually gives a hint to their personal motivations that are explained later.
The act of shooting John means that Cassian is definitely willing to kill the man who assassinated Gianna.
John's act of disarming the gun first means that he is willing to spare Cassian, which can be quite Out of Character as compared to most of his CQC fights against other assassins - specifically when John steals guns to kill his targets when he's unarmed. After the train brawl, John does spare Cassian's life, albeit with a knife lodged at the latter's artery.
When John stabs Cassian, he makes a point to tell him that if he removes the blade, he'll bleed out and die. With Ares, he stabs her in the same spot, but he deliberately pulls out the blade to kill her.
After Gianna commits suicide and John shoots her in the head to make sure he gets credited for the kill per the Marker, pay close attention when he's leaving the room and encounters Cassian. Cassian's question "You working?" and John's subsequent confirmation of it alone seem to be enough to lead to him and Cassian shooting, which seems like it's not 100% certain to have damned John for being Gianna's killer. But... if you look closely at John's face, he has drops of her blood on his forehead. That's what clued Cassian in that John was "working." And while he could have been there to kill anyone at the party, note where they met: John was walking from Gianna's quarters, making the conclusion as to who John was there for obvious. Cassian saw John with a bit of blood on his face, walking away from Gianna's room, and put the clues together immediately. All he needed was confirmation by John himself.
Speaking of Gianna's suicide, John shooting her serves a dual purpose. Not only does it ensure he gets credit for completing the job, but it also ensures that she can't take him by surprise if he turns his back on her before she's all the way dead. While naked and bleeding from both wrists in a bathtub seems pretty certain, John didn't slit her wrists, and the entire film franchise is based around the dangers of underestimating seemingly harmless people.
When John is prepping for the mission to kill Gianna, he stops to leave guns at two positions in the catacombs. Later on, after escaping from the castle into the catacombs, John is walking down a passage where he encounters Ares and her men attack him. John retreats back up the passage he was just walking down and takes an alternate route that takes him directly to his weapons, which he then uses to shoot his way back out of the catacombs. John not only prepared to fend off a possible ambush, but he'd completely planned out an alternate egress in case of an ambush.
Not only that, but it indicates that John was fully aware that Santino was going to screw him over the second the job was done. Anyone pursuing him after killing Gianna would have been coming from the same way he had, back through the party, while only someone who'd followed him from the other end would have been in position to ambush him on the way back out of the catacombs. John laid out his weapons in anticipation of being cut off by Santino's attempt to tie up loose ends.
During the preparation scene, when John visits the mapper, he pays the mapper four coins instead of a single coin he gives to Angelo for his armored suits. Angelo provided only a single service, while the Sommelier only recommended weapons and was part of the services John had already bought at the Continental when he checked in. This is because, if you watch closely, the mapper actually provided John four services:
The old blueprint for the D'Antonio estate.
The modern blueprint of the estate.
A map of the catacombs underneath.
The keys to unlock the gates.
Whenever someone speaks to John in Italian, he pauses for a moment before replying, and he only replies with a single Italian word. Contrast this with the first movie, where John doesn't hesitate when replying in Russian and speaks it fluently. This is because while he understands Italian, he still has to translate it in his head, while he's completely fluent in Russian because he worked closely with Viggo for many years, and as later revealed in Chapter 3, was actually from Belarus.
When John left his dog with Charon during his mission, the dog was benefiting from the Continental's protection. This would have likely been a wise decision even if his house hadn't been destroyed by Santino.
On a side note, if Charon is the ferryman to the underworld, this makes the dog Cerberus.
Everyone who has seen the first film has asked why didn't Viggo put Iosef up at the Continental so that John couldn't kill him. This film answers that question: because John didn't have anything left to lose and would have killed Iosef anyway.
The third film shows the apparent hypocrisy of the High Table punishing the Bowery King for aiding John Wick's retaliation against a member of the High Table before he was deemed excommunicado, even though Santino had done the same thing earlier in the film. But considering their penchant for fitting punishments, the line of thought may have been: Santino used John Wick to kill a member of the High Table, so his punishment was to deal with Baba Yaga coming after him next.
Between the first and second film, Wick seems to have Taken A Level In Badass, with much more fluid moves and a more elaborate combat style despite the sequel starting immediately where the first film left off. While in reality this is due to the fact that Keanu Reeves went through extensive training in preparation for the sequel, it can also be explained in-universe as well: Wick had been retired for several years by the time events were set in motion in the first film, so he was a little rusty. However, his training and experience came back to him as he slipped back into his old self, letting him re-acquire tricks and skills that had gone unused for years.
When the Bowery King ominously tells John that John owes him, John subtly advises him not to go down that route. At that very moment, John's literally on a path to kill the person he has owed an unbreakable favor to.
"Without rules we are animals." While it looked like simple platitude, how much worth is there in the Continental rules if Santino and Harry died in a relatively close time length in the same neutral ground? While Perkins was made an example of, Wick got off easily for killing a high-profile person from a group that can go to war with Winston if they saw his system failing and that assassins are breaking them left and right these days.
If the ending scene of John being Properly Paranoid at the park's bystanders is any indication, then anyone you've known could have worked for the Continental. All you have going for you is that nobody is putting a contract on you.
, both the painting and the actual event: A powerful political figure is cornered by an assassin and dies. Said political figure's death is the spark that lights the fuse that leads to a massive, insane political upheaval, befitting the implication that there's a war between the High Table and the Bowery King. And while Marat was assassinated and Gianna technically committed suicide, the famous painting evokes the sense of suicide.