Next up is
@EternalSunset0 's "Rise of the Shield Edgelord"
I went a bit far in some areas and idk where you draw the line between rewrite and simple straightening, but here you go.
General
After reading the first volume, I am very much inclined to agree with your self-evaluation. Your story does very much feel similar to the anime back then, as far as supernatural harem is concerned. Too much so, perhaps. Fitting both the ode to your favorite works and a total game changer into a single story would be insanely difficult, but even smaller twists remain missed.
The shield is a prime example. Within the genre at least, it was original, but its defining element, defense over offense and thus necessity of teamwork, got sacrificed for the "power of emotions" idea taken from your references.
Telling you that your characters feel mostly like tropes probably just reaffirms your own opinion of the topic and you asked me for suggestions on that specifically, so I'll try what I can do, but keep in mind that the more you adhere to my offers, the less it will me
your twists.
I have no idea where you are planning to go with them however, so I might be off by a long shot.
Characters
Kazuki Arata's originality as of now would be that he doesn't really have one. He had his own downfall and resulting seclusion, but the cause is a mundane one. No secret bloodline or locked memory busyness (yet?). There's also the otaku/gamer immersion aspect, but without developments that go against established tropes, I feel that his commentary is wasted most of the time.
He changes a bit too quickly imo. Entering the Mu as Mr. "Behold the fields on which i grow my fucks", he leaves as the principled and meddlesome MC, memory wipe or not.
Sayaka Uehara's trope is ice cube. Outwardly controlled and distant, those characters reveal a painful past or a girlish side once approached, often both. Since the design already includes subversion, it's kind of hard to add much while keeping the core idea. Perhaps work in the manga thing and make her a closet otaku? A bit of a stretch, but what better fantasy than the popular girl being into the same degenerated shit you are?
She'd try to hide it, but sometimes blow her cover due to involuntary reactions (giggle at a reference etc) (And I don't have to witness the making of yet another plushy lover ice queen)
Miki Amagi, as of now, appears to be the most well done character. It's clear to the reader that she's into Arata bc that's what they expect, but him not noticing feels justified as well with how she organically fits in between the MC and comedic relief. Certainly an engaging expansion to the gentle/popular/crushing tropes of childhood friends.
I'd expect her to be disinterested in manga/games herself, but do superficial research to follow conversations with Arata, so perhaps occasional slip ups? That'd be just a side aspect, though, nothing major.
Dr. Shin Kagami falls a bit short for the first villain imo. This might just be personal taste, but the immortality/advance of human race motivation has been a bit overused; the same holds true for the protagonists' take on the topics.
The novels you named as references stress/sell carving one's own path, whereas this argument is handled so one-sidedly that I don't really feel like I'm given a choice regarding what I should think. Later adding the fact that this goal entails ruthless selection does not only reinforce this, but also kind of contradicts with his motivations. A man who grieved for every life he failed to save should suddenly turn into a coldhearted utilitarian?
A possible rework regarding this issue (going solely off of VOL1) would be changing the target of his drive to children/future generations. A child died under his care, perhaps his own, but a patient should do as well, leading him down a path where he considers any sacrifice of the living excusable so long as they leave a better world for those to come.
Plot
As far as pacing goes, the first volume rushes through the supernatural part of the story. You have the "fateful encounter", saving Amagi and next up is the final battle. Don't get me wrong, an unexpected challenge causing the two to grow closer certainly is a good way to end the book, but already having them face off against the culprit behind the disappearings only to pull the villain escape to preserve the character feels sub optimal to me.
Perhaps two B-Class in quick succession? Up to you and whatever plot restrictions you have from the second volume.
(This perhaps is an issue stemming from the fact that you orient yourself with the help of anime, which by design have quicker advancement than novels. If you can give the MC and plot development a few more stops in between, it'd help a lot imo, even if they were to be cut in a hypothetical anime)
The daily life part has no pacing issues from my perspective.
What remains is character motivation. The MC
just having to return Uehara's card ASAP, even to the point of borderline stalking feels almost comedic, but him not passing his interview to his sister is just a bit of a stretch. Best fix would be him trying to give it to her beforehand, which she rejects, but I can't really find another solution.
I don't understand Uehara projecting her brother onto him however. From what I remember, he appeared to be a "strong until he wasn't" kind of person and as his sister, she should have never received most of the cold front.
Both of which she experiences in reverse with the MC, so while plausible in hindsight, she slips into this rather readily.
Hope that helps you in any way.