Every time you enter a new floor, the previous floors rooms are reset. As Sora and the gang advance through Castle Oblivion, they begin forgetting important things. Meaning, they forgot how they set up the rooms and need to set them up again.
Once you know the basics of the plot, if you start Sora's storyline over, it becomes hard not to notice that pretty much every world's modified subplot deals with the manipulation and falsification of memories. Considering the circumstances, it is entirely possible that Namine is trying to send coded warnings to Sora that he's being brainwashed.
It isn't until after you play through the game that you realize Aerith's speech to you at the beginning of the game may be Naminé sending a direct message to Sora, warning him of what lies ahead. Naminé is shown to be able to directly influence characters she creates, and Donald and Goofy tell Sora that they only saw him standing there by himself. In fact, if you pay attention you notice that Aerith is seen walking away first with the others only to suddenly turn around and talk to Sora by himself...
The Riku Replica's bizarre Jerkass behavior and desire to fight Sora for what appears to be no good reason should send up red flags that he's a fake, but doesn't because this is exactly how Riku acts throughout the entire first game. The subject of his anger at Sora has simply been changed from Kairi to Naminé.
However, it does seem to be a case of Flanderization...which, of course, also makes total sense given that Naminé was made to re-arrange his memories so that this would be the case. It's the same with Sora...Kairi is deemed the most important person to him, but Naminé starts to exceed that as the only important person to him the more fake memories based on his feelings for Kairi that are planted in his head. Both Sora and the Riku Replica are flanderized so that they are total puppets to Naminé...and thus, to the Organization.
Marluxia's Viewer Gender Confusion makes a whole lot of sense when you consider that Marluxia was originally conceived as female.
It's been noted that Larxene seems more like just an Alpha Bitch to the point of being Laughably Evil when around her fellow Organization members, but suddenly becomes extra-evil up against Sora, Donald and Goofy. Then you realize that Larxene is a sadist who gets off on inflicting pain on others' feelings...and the rest of the Organization don't have true feelings, just like her, so she has no reason to go as far in being cruel toward them. Even in RE:CoM, a moment is added when after taunting Vexen and causing him to shout at her, Larxene looks disappointed and says "Predictable response. Forget it. Men without hearts are so boring".
For the I.5 HD ReMIX, the fandom rejoiced when Kingdom Hearts received re-recorded tracks - and raged upon learning that Re:Chain of Memories not only didn't receive re-recorded tracks, but it didn't use the already re-recorded tracks for I - instead, the HD version of Re:Chain uses the PS2-generated songs from the original release. Then you remember: this is not actually one of Sora's adventures, it's an imitation of his previous adventure. Castle Oblivion just couldn't get the audio right. The exception is the battle with Marluxia: the... last? phase of the fight does receive a re-recording, signifying that he's breaking free of the imitation and finishing his adventure properly.
Also note that "Lord of the Castle" (the re-recorded song) is the only one that wasn't in the GBA version of the game.
In Kingdom Hearts I, the Powerwild and Bouncywild Heartless were found in the Deep Jungle world. Because the rights to Tarzan were lost before Chain of Memories, those Heartless are now found in Olympus Coliseum; the only world not to have any world-exclusive Heartless in KHI. Also, coliseums often contained wild animals, so their presence is more fitting than one might initially think.
In Reverse/Rebirth, Riku gets pre-arranged decks for each world (and each boss fight outside of the worlds). In Wonderland, Riku gets an extraordinarily sucky deck with less cards than normal and no cards above 5, whereas in Halloween Town for example, Riku gets an awesome deck with plenty of 9's, 7's and 0's. The fridge brilliance here is that Riku gets his power from Darkness. In a saccharine world like Wonderland, Riku is significantly weakened, while in dark and spooky Halloween Town he is significantly stronger. It goes even deeper, too: The mechanics directly support this, and so in Halloween town it is a piece of cake to break enemy cards and activate Dark Mode, whereas in Wonderland it becomes nigh impossible unless you carefully manage your deck.
Riku's deck in Olympus Coliseum is similarly constructed: it's built around the Powerwild enemy card exclusive to that world, which reverses the values of every non-zero card in your deck. If you don't know this, Riku's deck in this world is terrible; lots of low-value cards (including almost-useless 1's) and not enough 9's to complete a Dark Aura. If you do know about it, you can use Powerwild to get all the high-level cards you need. Why use this deck for Olympus Coliseum, then? Because it's an outwardly bright-and-cheery world literally sitting on top of an Underworld full of darkness. All you need to do is flip the table, which Powerwild is designed to do.
In the Re:chain remake, several of Sora's Sleights were changed, giving him attacks like Magnet Spiral, Firaga Burst, and Freeze. Not to mention his numerous "Raid" variants, Holy, and Tornado. Now go play Birth By Sleep. Those are Ven's attacks — Sora's heart is reacting to Ven's sleeping body inside Castle Oblivion, and the deeper he goes, the more of Ven's abilities he gains access to. This is also why Sora loses those attacks come Kingdom Hearts II.
There are a lot of subtleties to the way cards are used by the various characters in this game.
Notice how only humanoid bosses use red and blue cards instead of the black cards used by the Heartless and (most) Disney bosses.
In addition, the only characters who use cards that don't just represent themselves is Sora (and Riku, but only with enemy cards). What's Sora's special power, again? Linking his heart with others.
In the Game Boy Advance version, using Dark Mode for Riku is pretty much the easiest way to beat the final boss - and essentially something you have to do if you want to win. This actually is a case of Gameplay and Story Integration - by this point in the story, Riku has accepted his darkness, and the only way for him to win is to use the dark powers against the boss.
Additionally, Dark Aura. It's seen as Riku's ultimate attack, and was That One Attack in the first Kingdom Hearts game. Back when the game was first released, many first-time players were glad to see that was in Riku's attacks, but disappointed that it cost three nine-value cards to use, thus was exceedingly rare to be able to pull off... until Twilight Town and Castle Oblivion. What changed then? Simple balance since Dark Aura is actually still pretty powerful (though not as much against bosses...)? It's not - it's Gameplay and Story Integration. By this point, Riku has accepted the darkness within him. It's such a high value because he's afraid of it. Even at the end, he's still kind of afraid of it - hence its cost.
There is yet another case with Riku and darkness. The Maleficent Enemy Card strengthens Attack Cards at the cost of reload speed... except that Riku reloads cards instantly, which means that the Maleficent Enemy Card is a free buff. Maleficent is again incentivizing Riku into using her power... that is, the power of darkness!
Several of the Nobodies in this game act considerably more emotional than the ones in Kingdom Hearts II, showing strong reactions ranging from fear to joy to anger. Axel even remarks on noticing he's enjoying the situation. While this seems like Early Installment Weirdness when compared with the more coldly sociopathic Nobodies in II, it ends up foreshadowing the twist in Dream Drop Distance that Nobodies can grow new hearts.
When you really think about it, each Memory World in Sora's storyline (with the exception of Traverse Town, Twilight Town, and Destiny Islands, all of which are directly connected to the plot) foreshadows the story, Naminé's character arc, and the effect true and false memories can have on people:
In Agrabah, Aladdin is a Street Urchin who hopes to use the Genie's lamp so he can be with Jasmine, believing she wouldn't want to talk to Aladdin if he wasn't a prince. Jafar used him to get the lamp for himself so he can use it become Sultan of Agrabah by making Jasmine his queen. Aladdin realizes if he does go through with his plan, he'll be no better than Jafar, so he ultimately chooses to instead free Genie from the lamp before going to meet Jasmine, wanting her to know the real him. Naminé, while she was forced by the Organization to manipulate Sora's memories, admitted she used her powers to draw Sora in to escape her lonliness, but finally acknowledged it was wrong and instead to chose to do the right thing and tell the Sora the truth and restore his memories, which allows them to promise to meet each other again someday as real friends.
In Olympus Coliseum, Cloud makes a deal with Hades. In exchange for eliminating Hercules, Cloud will have his memories restored. When Cloud fails in the task, Hades double-crosses him, never intending to help him in the first place. After Sora defeats Hades, the games are cancelled due to everyone being in no condition to fight, much to Sora's disappointment. Before Cloud leaves, Sora tells him that the smallest things will help bring back memories, since even the most important ones aren't gone forever. Riku Replica fought against Sora due to being led to believe he was a threat to Naminé, unaware that the Organization had Naminé mess with his memories and used him as a pawn to lure Sora further into the castle. Sora and his friends' memories have been messed up to the point they have to sacrifice the memories they made at Castle Oblivion to recover them, including the recent memories of Naminé despite finally meeting her, necessitating they sleep for a whole year. Sora is able to recall Kairi, his most important memory, just by looking at her good luck charm instead of the false one Naminé made and thinking hard enough about who the red haired girl is.
In Wonderland, the Chesire Cat gives the group advice about how to deal with the Queen of Hearts, "Think too hard, and your memory might lie to you." Alice makes the Queen of Hearts believe she ordered Sora and his friends to destroy the Heartless, exploiting her lost memory and counting on her being too prideful to admit that didn't happen. When Sora thinks too hard about the girl that suddenly appears in his memories, he was led to believe in false memories of Naminé, something that was exploited by the Organization.
In Monstro, Pinnochio tries to find an exit out of Monstro without telling Gepetto because he didn't want him to worry, only to be encouraged by everyone to tell him the truth instead. Sora also encourages him to fight back against the Heartless holding him captive. Naminé does fear Sora wouldn't like her if he knew the truth, but still told him anyway and is surprised when he still wanted to help her. This gives Naminé the courage to defy Marluxia.
In Halloween Town, Dr. Finklestien's potion is supposed to bring back true memories, but when Oogie Boogie drinks it, he is overcome by fear. The doctor theorizes this is because true memories unbalance the heart, and if Sora had drank it, something even worse would happen. When the Riku Replica regains his memory of being a replica of the actual Riku, he becomes unbalanced trying to become his own person due to Axel's manipulations.
In Atlantica, Ursula uses Ariel to get the trident by taking Flounder hostage and making her think he's been abducted by humans. After defeating Ursula with the help of Sora's friends, she decides to tell her father the truth and take responsibility rather than put all the blame on Ursula, despite being afraid of getting into trouble. Naminé, even though she was forced by the Organization to mess with Sora's memories, still vows to take responsibility and make things right by restoring Sora's memories at the cost of making him forget her rather than let him continue to live a lie, despite knowing how painful it is.
In Neverland, Peter Pan doesn't want Wendy to return home because she'll forget him and everything they went through together growing up. Sora tells him that memories aren't truly gone and that the right trigger can bring them back. Even though Naminé replaced Kairi in Sora's memories, he could never truly forget her, and was able to remember her with the right trigger. There's also the fact that Peter throws a tantrum and leaves Wendy when she first tells him she wants to go home, which is acknowledged by everyone as an act of immaturity just because she didn't want to do things his way, foreshadowing how Sora would abandon Donald and Goofy when they try to tell him to think about the suspicious circumstances of his memories of Naminé.
In the 100 Acre Wood, Sora helps Pooh find his friends, who aren't far. While they do part ways and Sora fears he'll forget, Pooh Bear assures him he won't forget him. Sora came to Castle Oblivion believing Riku is there, and while that is the case not long after Sora enters the castle, he never finds this outnote In the orginal GBA game, it's possible to miss some of Pooh's friends on the way.. When he starts to think about Naminé and where she disappeared to, he soon discovers she's inside the castle. Even though Sora has to forget her to regain his memories, Naminé will still remember him.
In Hollow Bastion, Belle is taken hostage by Maleficent to lure the Beast to her so she can steal their hearts the moment they show their love for each other, forcing Belle to act cold towards him to keep him safe. Even after learning that Belle was only cold to him to protect him from Maleficent, Beast still vowed to come to her rescue. Naminé was used by the Organization to lure Sora to them, and even though Sora learns she had tampered with his memories, he still vowed to save her due to knowing she's a victim just as much as they are.
In the game, many of the Enemy Cards of story important characters actually make sense to who they are or are fitting to their parts in the story.
Riku gives Sleight Lock, which allows you to keep the first card you'd normally lose in sleights for 5 sleights. Although this card is given by the Replica, it fits Riku's character arc. He originally wanted to get rid of the Darkness, fearful of being taken over by it and being controlled by Ansem once more. But as the story goes on in CoM, he begins losing his fear of it and approaches it in a more healthy manner. What he'd otherwise wish to lose instead remains as part of his strength.
Ansem has Sleightbind, which in the original game conceals your deck and cards from opponents, but in the remakes it instead grants resistances to Fire, Ice and Lightning. These both fit Ansem. The first version fits as Ansem, being part of Xehanort, had hidden his true agendas behind his masquerade as a heartless as well as Ansem's original desire to reveal his "concealed" memories. The latter portion fits in the sense that Ansem has proven notoriously hard to kill and gaining resistances reflects that.
Xemnas has Quick Barrier, which guards from consecutive attacks and confers resistances to Fire, Ice, lighting and special attacks. This also seemingly reflects Xemnas's connection to Xehanort in how there always seems to be one more backup plan that can be set into motion, guarding from losing the original goal. As well, it confers the same resistances and abit more than Ansem's card does, reflecting the connection and improving it as Xemnas likely has more of a mind than his Heartless self.
Vexen gives Auto-Life, which revives you automatically if your health hits 0. It also grants you immunity to Ice, but makes you weak to fire. Vexen did create the replica program, making it possible to create more bodies for people to inhabit and evidence is shown within this game. The fact that he's weak to fire also fits with his death by Axel.
Lexaeus gives Warp Break, which can obliterate enemies on a finishing combo strike and grants immunity to ice, resistance to Physical attacks and makes you weak to special attacks. This seems to fit his enormous strength and his connection to Vexen, but granting weakness to special attacks is fitting due to being killed in a way he didn't see coming (Ansem-possessed Riku).
Zexion gives Confu-strike, which confuses foes at a certain rate while giving resistance to fire, ice, lighting and special attacks. This fits how he tried to manipulate Riku by appearing as Sora, attacking him emotionally. Furthermore, the resistances gained is the same as Xemnas's, giving the connection of how capable Zexion is as a member of the organization.
Axel has Quick Recovery, which allows you to use your cards even while staggering from damage. You also become immune to fire but weak to ice. This fits in how Axel manages to keep pushing things forward plot wise despite being damaged or hurt. From his fake death to Sora, to losing Roxas, until it's finally subverted with his final death in Kingdom Hearts 2.
Marluxia grants Double Sleight, which allows you to use stocked cards and Sleights twice in a row. It also grants resistance to Fire, Ice, Lighting and Special Attacks, but makes you weak to physical attacks. If read literally, "double sleight" can be renamed to "double slight", a slight being a disrespectful insult which fits his disrespect of the Organization. It could also refer to him "Double crossing" the Organization. It also serves to mention that the resistances it grants his the same as Xemnas's, showcasing he has an equal level of power to him, but it also grants weakness to physical attacks, showcasing how Marluxia is still the potentially weaker of the two.
Larxene grants Dash, which increases running speed, grants immunity to Lightning, but weakens you to Special Attacks. Larxene is known for her speedy assaults and giving people the run around to rile them up and torment them.
It seems odd that Sora would learn Quake in Re:Chain of Memories when most of the abilities he gains are Ventus's and Quake is one of Terra's. Ventus had the ability to D-Link with Terra and while he never actually used Quake, it did give him access to one of Terra's earth-elemental finishers. Given that memories in the Kingdom Hearts universe are a function of people's connections with each other, Sora likely got Quake third-hand from Terra thanks to Ventus's strong bonds with the latter.
Notably the altered plotlines mention no connection between the villains. There is no grand conspiracy between Hades, Hook, Maleficent, and the others. While many points show that Namine is probably altering the story to give Sora a warning of DANGER!, she is being made to do so by Marluxia. He probably can tell her to leave or add certain aspects to the false memories, and why hint at a conspiracy or secret cabal when you want Sora to serve your conspiracy or secret cabal, especially as such an alliance would be seen as a bad thing in the false memories.
While Traverse Town, Twilight Town, and the Destiny Islands are directly part of the main plot in Sora's storyline as mentioned above, they do foreshadow some things that would be revealed in Kingdom Hearts II:
In Traverse Town, Leon and his gang do not recognize Sora and his companions initially, but are able to remember their names and Leon's parting words back in Hollow Bastion with some prompting, despite claiming to have never met them. Aerith theorizes this is because Sora's heart is connecting them and doing the remembering for them. We would later learn in the next game that everyone forgot Sora's party at the same time they forget them as a side effect of Naminé tampering with Sora's memories, and it's not until their forgotten memories are restored that they everyone else remembered Sora's party. So in a sense, Sora's heart really did connect them all.
Twilight Town quite obviously foreshadows Sora's connection to Roxas, namely how Sora has a sense of nostalgia despite never having been there before, and Vexen's statement about how the "other side of Sora's heart" remembers.
On the Destiny Islands, after Naminé shatters the illusion created by the false memories, Sora is able to recall Kairi's existence, despite not being able to remember her name until he's just about to go to sleep. The next game reveals that Kairi was the only one on the Destiny Islands that could remember Sora existed but was unable to recall his name and face until she received some prompting from Sora's voice. This clearly shows how close Sora and Kairi are to each other.
Unlike Sora, Donald and Goofy, Riku and Mickey don't get new costumes for Halloween Town (merely having their default outfits get slightly darker, duller and more detailed). While out-of-universe, this is likely because the developers didn't feel like creating new outfits for what would ultimately be a tiny portion of the game, in-universe it could be justified as both Riku and Mickey already being aligned with darkness (compared to Sora, Donald and Goofy) to the point where they don't need to significantly alter their appearances to fit in with the Halloween Town residents.
Alternately, since Halloween Town in COM isn't the actual world but rather Sora's memory of it, Riku and Mickey don't change their appearances like they might have if they visited the actual Halloween Town because Sora never met them there and so has no preconceptions on what they'd actually look like if they visited.
Popular theories are that the potion made him "remember" that he's just an illusion that will disappear once Sora leaves the floor... or that the potion made him remember the real Oogie's memories from the previous game... including the fact that Sora and Jack essentially destroyed him. It could be the reason why his memories were out of wack in II.
Marluxia plan is this when you realize how close he was to turning Sora into his puppet. Had Axel not let Namine go, Sora would've been doomed to be Marluxia's slave forever.
A single line here that spreads across the entire series: in a relatively lighthearted scene, Sora jokes that Donald beat him up when he was a Heartless without realising it was him. Here's the question: how could he remember thatunless he was conscious of what was happening?
Much earlier in game, when you finish the first floor and get in front of the second floor, a cutscene plays where Goofy attempts to recall Hollow Bastion, but while he can recall how it looked like, he can't recall the name. Sora and Donald both fail to recall it completely. This begins to highlight Namine beginning to remove their memories, but take note of another fact... when you get to the upper floors where you will have the Hollow Bastion card, none of them recall the earlier conversation nor does it seem to come up. The Fridge Horror that can be taken from this is that Namine's memory wiping is getting to the point that not only have they completely forgotten their previous adventure, but it's starting to make them forget their current one too.