Sara paying the Cerise Institute a visit before running away from home might seem like a colossal bad move, but it makes a little bit of sense: the Routes around Vermillion City are surrounded with tall grass, where Pokemon live, and since this is based on the anime, those can get really territorial with the wrong step. Getting a Pokemon is just the logical conclusion since Sara doesn't have one of her own and can't hope to match a Pokemon in power. So while it's still a bad move, it's better than heading into the wilderness and being skewered alive by territorial Pokemon.
The story tries to paint the Infinity Train as having a Double Standard regarding how much it values Denizens and Passengers, emphasizing the latter over the former. However, this makes more sense when you consider that the Denizens are literally created by the Train, and as such, they can be reconstructed even if they do die. Passengers, meanwhile, are a one and done deal; they die, that's it. There's no coming back. So of course the Train would prioritize the safety of objects it can't bring back from the dead so easily.
This is without mentioning the fact that the Double Standard would need the Train to operate on a normal morality to work. Which it doesn't; it literally kidnaps people to turn them into Passengers and force them to face their issues, and if they die in the process, they get turned into Denizens regardless of their previous history. The Train operates on Blue-and-Orange Morality, so trying to uphold it to the average moral standard required for a Double Standard is unfair.
Notes are made in story that the leaders of the Apex are somewhat Book Dumb: being on the Infinity Train since they were about 10. While the story's not made a specific note about it, there is someone who is also Book Dumb who's been on an adventure since he was 10: Ash. The group have many differences of course: Ash doesn't corrupt those around them nor goes off destroying things needlessly. Their settings are also a major difference point: Pokemon trainer is something of a life style and career that, while not a cake walk, is something that the Pokemon World is designed for, letting people with the ability to succeed at the task to do so for as long as they are able and wish too (from ten year olds to elders like Alder, Agatha, and Opal). The Infinity Train is not meant to be a lifetime path as Grace and Simon have been using it, thus problems upon problems.
Of course Chloe is having trouble admitting fault after the Cyan Desert, unlike her Blossoming Trail self; she was less directly involved in the fiasco. That Chloe had all the egg on her face because she basically made Parker into the monster that he was. This Chloe doesn't have the same responsibility about Sara, making it easier for her to give herself more 'high ground' than her original take was able to. She has the wiggle room to (attempt) backhanded apologies that, if the original tried, would have ended rather badly for her.
Chloe taking Specter's advice over Sycamore during her breakdown seems pretty cruel, and it kinda is, but it makes perfect sense when you think about it: As the original trilogy shows, treating Chloe with kindness during her train trip more often than not led to the redhead twisting and contorting the kindness to seem worse than it actually was, no matter how sincere it is, in order to have a reason to reject. Meanwhile, treating her with bluntness and even a little cruelty proves key to getting her to realize how not only is it genuine, but how she has to change herself in order to get anywhere in life. As a result, while Sycamore's kindness managed to get this Chloe to open up, it simply couldn't help the girl get over her wrath and spite over what happened at the Cyan Car, while Specter's blunt callout got her to realize what an idiot she was being and how she needed to change in order to get out of the Train and go back home.
While still frustrating, Chloe's inability to apologize makes sense when considering her previous outing with Professor Sycamore: the man's kindness failed to get through to her, and Chloe, in a moment of spite, used him as a venting toy until he snapped, causing him to go insane. Ash is similar in that he's a perfectly Nice Guy who was nothing but cordial with Chloe, but she took his kindness and twisted it. Her having a hard time apologizing to him could very well be her anxiety over messing things up like she did with Sycamore, especially with the consequences being implicitly worse should it happen.
Of course Chloe would freely admit she's no different from Sara's mother: if the story makes something about the Dyktalises clear, it's that they're too proud to admit they're in the wrong. By agreeing to the idea that she's as bad as her [Sara] mother, Chloe's essentially gaining the moral high ground over them, which is something she desperately needed after her failure with Sycamore.
Chloe and Sara's interaction is actually a good foreshadowing for Sycamore's later reaction: Chloe tries to repeat what the professor did; take a pacifistic and diplomatic approach, while telling Sara that she can be better. Sara's response? To try claw her own throat out, utterly refusing the kindness she was shown just like Chloe did with the professor moments ago. The difference is that rather than being whisked away to a situation where her ego can adapt and make herself seem like the innocent victim, she's being sent back to reality to face the fact that her actions have consequences.
After the fiasco of the Cyan Desert Car, Sycamore refuses to accept the apologies people give him, especially Asher and Chloe's. Why's this? Look closely at the apologies themselves; while they do apologize for what they did to him, it doesn't take long for the apology to derail into what they did and how they should've been better. This is the exact same thing Sycamore did, try to apologize sincerely only to get carried away and promptly rejected. The apologies fail not only because Sycamore needs to work on himself, but because they bring him bad memories.
Chloe having taken Goh on a ghost hunt that went horribly wrong gives some depth to her issues with Ash. Ash is no stranger to taking Goh on adventures, several of which include Ghost-type Pokémon (i.e. Gengar, Cofagrigus, Golurk, and Phantump). However, it's been established that one of Ash's top priorities is the safety and wellbeing of his friends, human and Pokemon alike, and will drop everything to help them if he thinks they're in danger. Meanwhile, when Chloe had an adventure with Ghost-types and Goh, he nearly died and his parents grew to hate her because she cared more about wanting to do another ghost hunt rather than show concern for Goh's health, regardless if she saved his life.
Parker tries to show the adults how to confront the Shadows by going up to his own and accepting it. Thing is, this only works because the Shadows work on Persona rules. What would've happened if they looked like it but operated on other rules?
By the time Act 1 ends, Chloe has essentially broken Professor Sycamore beyond repair, with the man having to be reset just so he doesn't destroy the world. How is Rimuru going to take this?
In order to stop him from rewriting the universe again, Paimon is forced to reset Professor Sycamore back to once he was. How did this affect his number? Has it gone back to normal too or is it still the same as before? Did he become this verse's counterpart of a Static Passenger?!
As the Palimpsest Car draws to a close, Tres tells Chloe that Sycamore, in order to truly heal, has to work on himself. Given how broken the man is, however, who's to say he's even going to try and not go down the same road as Chloe; refusing hope because of how easy it has been proven to him how quickly it can break?
In a very somber way, Sycamore was right; most of his breakdown and general increase in cynicism and pessimism only came about because Chloe rejected him when he just tried to help, and not in a normal manner, but a particularly brutal and emotionally damaging one. If Sycamore had just showed sympathy for Chloe's plight and didn't have the Windchasers join forces with the Red Lotus Trio, he wouldn't be the mess he is today.
Ash decides to leave Vermillion City with his Pokemon in order to go to Alola. All fine and dandy... until you realize what a broken mess he is and how Sara has left him feeling like he can't do anything to help. Who's to say Alola won't be his final regional visit before he decides to quit on his dream and give up on ever becoming the very best like no one ever was?
Given how much better spirits he is when he is Alola, he'll be fine.
The reveal that Goh's parents have been deliberately driving a wedge between Goh and Chloe puts their actions among this story in a much darker light...
During their later talk in the Harvest Moon Car, Goh ends up promising Chloe that he's going to go back to school until she returns from the Train. Given how the situation at Vermillion School has not improved at all since she left, Chloe essentially convinced her only friend to go into the same institute where she was bullied to depression in order to suffer the same things she did.
So what exactly makes Chloe so unique that the Train and One-One need to keep her protected in order to defeat the Apex and Cage of Flauros? If it's her supposed kindness, there are many other Passengers who are capable of showing the same level of kindness as her, if not even more so. And if it's all the power ups she's gotten, who's stopping other passengers from getting the same power ups?
So Tres is supposed to be a therapist, right? Considering the fact that Sycamore is not in a good state of mind and Chloe has proven to be repeatedly toxic and stubborn in her beliefs, why would any therapist suggest that they stick together rather than go their separate ways?
The Harvest Moon Car tries to paint Chloe as being one of the biggest reasons why Goh hasn't been kidnapped by the Infinity Train. How does this actually work, however, when the story has been very clear from the beginning that not only is Goh and Chloe's relationship so strained they're strangers, but the former barely even thinks about her?
Why hasn't Goh been expelled from school yet? It's made pretty clear he's an Apathetic Student for the most part, doesn't even show up to it outside of test days, and once Chloe is no longer there to deliver his homework, nobody, not even Goh himself, bothers to check if he's falling behind. Coupled with his parents not even bothering to check emails regarding the change of class, what's stopping the principal or any other teacher from simply deciding Goh isn't school material and booting him out?
Japanese schools are different from western ones. They have different rules and expectations.
He also is established to have special accommodations with the school. The only reason any problems exist is because of communication problems between the school, himself, and his parents; and Goh's clearly not the problem since he isn't the one ignoring emails or calls.
