Some of Date's behavior makes more sense when recalling his backstory from the first game:
Why does he prefer wearing masks of Saito? Because that's his face, the face of Kaname Date, ABIS agent, and not the face of an assassin drenched in blood who already made the choice to give up his past.
During the finale, Date puts a lot of emphasis on using stun bullets and then only aiming for the limbs when using real bullets. It's not just the usual 'heroic characters can't kill anyone', it's Date making sure he doesn't become a Killer Cop again.
Date's surge of power upon reading a Porn Mag being so much stronger than it ever was in the first game can actually be easily attributed to him being back in his real body - even if still styling his face after Saito by wearing a mask. It pretty much is the same reason Saito desperately wanted his real body back in the first game, to feel the rush his killings granted him, which was intimately tied to his own physical brain; Date needs the Falco body, the one who had the "White Snake Episode" as a child to be better attuned to their silly super power.
Though it's subdued enough to not notice the first time reading, Tama's mildly confused/annoyed response to Ryuki confirming Shoma being in ferris wheel car #2 on February 14th makes a lot more sense when you know that not only is this six years later from when he'd gotten on, but that Ryuki had resolved the situation himself at the time, and finding it 'important' now WOULD be weird.
Ryuki walking up the staircase to arrest Tearer seems like a bad case of Why Don't You Just Shoot Him? considering Date tranqs him on sight and Mizuki demonstrates at the start of the game that a stun grenade round can be fired 300 feet away. But two days prior, he shot at a costumed civilian and was severely chewed out for it with an upcoming demotion, of course he would try to properly verify this time.
The code in Tokiko's office at Naix Japan, 4901095, is a Goroawase Number that spells out "Shigure Tokiko" (4 = shi, 9 = gu, 0 = re, 10 = to, 9 = ki, 5 = ko).
A lot of Chikara's Somnium makes a lot more sense the more you learn about him. While most of it is Fridge Horror, there is a piece of Fridge Brilliance. He describes it as a simulation world that has no limits, which makes it seem like he is aware that he is in a Somnium rather than unaware of what is going on like most psync subjects. However, it is because he staunchly believes in the simulation theory as an avid believer in the Order of %. Therefore, his Somnium is how he perceives the world.
It may seem odd that nobody ends up telling Mizuki about how she looks a lot like Bibi. However, when you think about it, a lot of characters have reasons for doing so.
Bibi is never once shown meeting Amame, Iris, or Ota.
Moma and Lien recognize Bibi as "Quartz" and keep her status a secret as professional business partners.
Gen may not wish to acknowledge Bibi's existence since she almost exposed the corpse he had recently concealed during their first encounter six years ago. Additionally, Date was masquerading as Gen during parts of the present-day investigation.
Ryuki is mentally unsound and may not be consciously aware of their similarities, though he does make an off-handed comment to Mizuki during his recovering sobriety that he only sees two of her now.
Shoma only met Bibi for a short hospital period where Bibi relayed a backstory counter to what everyone knew about Mizuki at the time. When Mizuki offers Shoma a Valentines chocolate in one of the present day routes, he admits to a sense of déjà vu, implying that his memory of his encounter with Bibi is vague.
The timelines splitting made sense from Ryuki's side, given his mental issues, but it doesn't really make sense from the perspective of the Mizukis. that is, until you consider that it's not actually from the perspective of the Mizukis, but rather Aiba piecing her memories together after they were wiped.
When the game asks your permission to mention spoilers from the previous game, it demands you prove you're familiar with the first game by identifying Mizuki as the person whose leg was injured in the climax. At first it seems like a random choice to prove your familiarity with the first game, but notably, Mizuki's leg wound helps distinguish her from Bibi, foreshadowing her presence in the game. The question is basically teasing you with The Reveal at the very start.
Once again, the normally cheerful Sunfish Pocket is used as the setting for a nightmarish tragedy, being where Saito planted Renju's corpse in the first game and Amame's second Somnium which reveals her Dark Secret. It makes sense since Spike Chunsoft are known for games that have settings that look pleasant, only for everything to devolve into tragedy at the drop of a hat.
A new function of AI-Balls is the ability to project holographic models onto the hands of their partner in lieu of photos. It's likely that Boss pushed for this so she wouldn't have to print photos for Date anymore.
Somehow, the Annhilation ending from the first game gets even worse after you learn Boss' adopted daughter is Mizuki's elder clone sister, meaning that not only will Date have to deal with being unwillingly stuck in her body, he now has to break the news to the poor girl of her adoptive mother's death (said mother, it should be noted, he's trapped in) while Mizuki discovers that not only are her family and friends dead, but she's a clone herself. To say nothing of Ota's ending being even worse, as Saito is in Boss' body, and has access to an unsuspecting teenage girl.
Furthermore, assuming Saito decided to take over Bibi's body, Ota's route has the potential to be even bleaker than the Annihilation ending and that's ignoring the fact that he'd be in the body of a superhuman. If he were to take over her body, Saito would gain access to all of her memories. Now what would happen if he learned about Chikara and took an interest in his research on immortality...
The ending for Shoma and Andes route may appear happy at first as those two finally manage to get over their issues with one another thanks to Andes not dying. However, once you consider that Amame only killed Tearer out of revenge for her father's death, you know what actually happen to Tearer in that route as he could ultimately be a Karma Houdini.
Uru describes Amame in his journal as the person of his "destiny", and their encounter in the past at Dvaita ended with Uru sparing her life and wanting to teach her about Naix and the Nirvana Initiative. When taken everything to account, the game heavily implies that Uru was romantically fixated on Amame. While this explains why Amame killing him is the one thing that catches him off guard, it's especially horrifying to consider that his perception of love is so warped from his upbringing and Tokiko's enabling of his actions that he doesn't see how messed up it is to brag about killing the parents of his romantic interest — if anything he most likely perceived it as doing her a service.
In Bibi's Somnium, the canon route features an instance where Aiba has to re-enact Bibi attempting to save a stuffed rabbit from Chikara's experiments, which includes one instance where Aiba is forced to attempt preventing a drill from piercing the rabbit using her bare hands. Later in that same route, Bibi reveals to Mizuki that during their time at Horadori, the two of them had code names; Bibi was Mouse, and Mizuki was Rabbit. This reveal recontextualizes Bibi's Somnium in a harrowing way; the "rabbit" which Bibi was attempting to save from horrifying body experiments was actually a three-year old Mizuki.
Ryuki calling himself Half Might may seem as a case of Writing Around Trademarks. However, when you consider that he lost "half of himself" when he lost his brother, it's likely that he doesn't call himself All Might because he's not "all" there.
Amame Doi's initial Somnium arguably qualifies as one of the most unnerving Somniums in the entire series between the emotionless characters, loaded quiz questions you're asked to answer, the theme of distorted/destroyed objects, locations and people, as well as the complete silence slowly being replaced by a dark ambiance. The initial framing of the game's timeline makes this Somnium seem like it's taking place in the past and that she's sitting on a big secret regarding Tearer and his plans, but the Somnium is actually happening in the present — specifically in the days after she's already murdered Tearer. This reframes her Somnium in an extremely tragic way where the Psync Ryuki is performing is peeling away at her layers of guilt; the rapid questions being asked are her way of burying what she did under coping mechanisms of how different things could've been if she only answered the other way around. Perhaps most tragically, all of her friends and loved ones appear dead (both figuratively, and in the case of the spot-the-difference section literally) and flash by in distorted photographic images because she feels that she's betrayed them all by turning into a murderer. She's not only had her family taken from her, but now deprived herself of the loved ones she still had, and none of their words register as anything but hollow.
