Gwen, you do not have main character syndrome. Run. Leave.
You are going to die.
Another parallel- Colin goes to therapy like Melanie, and (just like with melody) the therapy sessions are a safe space that we as the audience cannot follow the characters into. However, Colin and Melanie diverge in the sense that Colin just keeps asking his therapists about computers and refuses any other kinds of help. While Melanie’s therapy helped her grapple with some of her fear, I think Johnny is trying to point out how therapy isn’t a magic fix all. That is to say, in order for therapy to work the person needs to actually want to be helped and by extension forcing someone without the right mindset or desires to go to therapy might not actually be all that helpful. Something that leads to drastically different outcomes for Melanie and Colin due to their personalities and desires.
Damn. The parallels are just going to kill me.
Some other parallels
“Gwen, you do not have main character syndrome. Run. Leave.” You are correct considering what happened to the real Elias Bouchard (he had his body quite painfully stolen from him).
Lena does imply that Gwen could’ve died in this interaction-
GWEN
“I thought he was going to kill me!”
LENA
“But he didn’t, which means you’ve passed the first part of your probation. Congratulations. Did you scream?”
Here we can see a couple similarities to Jon. A boss that seems to appreciate a worker that seems like they won’t die in addition to being someone that can witness the fear and horrors of the supernatural to internalize / comprehend them.
The second statement of Episode 1 of TMAGP seems extremely similar to the first statement of TMA in regards to the presence of something resembling the Anglerfish. Not only does it steal someone’s skin to impersonate them after an encounter in the night but when asked when Harriet asks “Arthur” if it’s really him he says “Some of him”, and when Jon asks Sarah Baldwin if she is still herself in MAG 096 (Return to Sender) we get this.
ARCHIVIST
“Are you the same Sarah Baldwin that disappeared in Edinburgh in August 2006?”
SARAH
“Some of her. Skin. A few memories. Not on the inside.”
Lena and Elias / Jonah are both bosses that supposedly murdered people that came out of hiding. Elias / Jonah murdered Leitner after he came out of hiding from the tunnels, but in Lena’s case it’s sort of reversed. Klaus says he can disappear again before Lena supposedly kills him but it is revealed that she actually helped fake his death and thus helped put him into hiding.
In the most recent episode (11) Ink5 mentions “Sutherland Macdonald” when talking about the tattoo Gordon and his crew uncovered. Sutherland is an actual historical figure famous for his tattoo work, which is quite similar to how Robert Smirke is a real historical figure and architect.
The cases Sam and co review are quite similar to the statements of TMA, and even seem to cause mental stress on certain people (Martin seems worn down from listening to statements, which Jon notices in TMA and Alice recommends trying to tune the talking cases)
Like in TMA, we the audience are perceiving the story through some sort of recording device(s).
Sometimes Sam gets cases that are conviently related to whatever he is looking into which resembles how Jonah left breadcrumbs for Jon via various statements and how Archivists in general could randomly “know” things. This also mirrors how Jonah left out files for “Nosie” Rosie to pique her curiosity.
In Episode 10 it looks like something was once again sealed / trapped under the Institute. Leitner trapped Not-Sasha in the tunnels under the Institute in TMA.
In episode 6 Celia quips “Four weirdos in a basement reading scary stories. Dream job.” This sounds like how one might describe the job of Jon and co in the basement. 4 weirdos (Jon, Sasha, Martin, and Tim) going over spooky stories in a basement or some other weird room (a basement or underground warehouse of sorts is not unlikely considering the access the characters seem to have to the tunnels under the Institute).
Gerard gives Celia and Sam a painting called “Camden Epiphany”. In MAG 004 a painting Gerry made of an eye is described as saying “Grant us the sight that we may not know. Grant us the scent that we may not catch. Grant us the sound that we may not call.” An epiphany is defined as “a moment of sudden revelation or insight” so one could argue the painting in MAG 004 is indeed related to some sort of epiphany or asking for one, and both paintings are potentially related to insight.
In Episode 10 we get this interaction
ALICE
“Ew. That explains the pattern on the floor.“
SAM
“Oh yeah… What is that?”
ALICE
“Worm tracks. Or y’know symbols of ancient otherworldly power. One or the other.”
Which is probably meant to be a cheeky nod to whatever the fuck the worms were doing in the Institute’s tunnels. Time even mentions “I didn’t stay long, ‘cause it had a lot of worms in, and they weren’t acting like the others. They were sort of… wrapping around each other, like they were trying to form a… thing, like a structure or something. A ring.” Entities, such as the Corruption could indeed be accurately described as an “ancient otherworldly power.” This is because the Entities exist outside of the physical universe and because they were sent to the Protocol universe from TMA.
There’s probably more but that’s most of the obvious ones I have. I definitely don’t think all the characters are 1-to-1, but this definitely feels like a JoJo’s Bizarre Adventure: Steel Ball Run type situation where there are certain thematic parallels or takes on each of the characters along with some nods or cheeky references.