Looking for some good whodunits

"Mucho texto" enjoyer
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Simple request. I love mysteries and am looking for more. Mysteries with other plot aspects are fine, but must be actual mysteries, not just stories with a hint of mystery here and there (there are a lot that come up when I search mystery that are more action or even completely separate genres). For instance, I adore Shion no Ou, a story about a young girl struggling to become a kishi (professional shogi player) and participating in a huge new tournament while haunted by her parents' mysterious murder years ago, which left her mute with vague and partly blocked memories. While she is mainly focused on shogi, a number of characters are far more focused on trying to identify the culprit, especially since he seems to be acting up again and extremely focused on the girl he let live.

I also adore whodunit series, where you have one mystery after another. See, for example, pretty much any work by Katou Motohiro or Shin Kibayashi, as these two authors basically made their names in this particular field. I'm fine with either way, whodunit series following a detective solving one mystery after another or stories that really consist of one singular mystery from start to finish. Or ones that are in between, like detectives dealing with mystery after mystery while simultaneously trying to uncover some larger, sweeping case. Regardless, just please give me good mysteries with good intrigue and at least a good semblance of standard deduction stories with clues and hints.
 
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Haven't read Shion no Ou,
but what do you mean by "stories with a hint of mystery here and there" but they are not "actual mysteries"?
what are examples of those?

Because to me, lately, Q.E.D.'s 'whodunit' stories feel like they are just magically solved.
I've noticed more convenient plots and less deduction, where suddenly this or that guy is revealed as the culprit.
Meanwhile, Kindaichi is pretty much a basic detective plot like Conan.

Do you count stuff like Kusuriya Hitorigoto as mystery?
How about Furitsumore Kodoku na Shi yo? Mitaraike, Enjousuru? Hen na Ie series? Theseus no Fune? Ubume no Natsu series?
"light" mystery like Boku wa Ano Yoru Ano Ko to? Isho, Koukai?
Do you fancy Fantasy like Eris no Seihai? Seijo ni Uso wa Tsuujinai?
 
"Mucho texto" enjoyer
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Haven't read Shion no Ou,
but what do you mean by "stories with a hint of mystery here and there" but they are not "actual mysteries"?
what are examples of those?

Because to me, lately, Q.E.D.'s 'whodunit' stories feel like they are just magically solved.
I've noticed more convenient plots and less deduction, where suddenly this or that guy is revealed as the culprit.
Meanwhile, Kindaichi is pretty much a basic detective plot like Conan.

Do you count stuff like Kusuriya Hitorigoto as mystery?
How about Furitsumore Kodoku na Shi yo? Mitaraike, Enjousuru? Hen na Ie series? Theseus no Fune? Ubume no Natsu series?
"light" mystery like Boku wa Ano Yoru Ano Ko to? Isho, Koukai?
Do you fancy Fantasy like Eris no Seihai? Seijo ni Uso wa Tsuujinai?
For stories that just "have a little mystery", take for example something where a girl is made a superhero and over the course of her plot has to figure out one or two minor key points while the real villain is right there at all times, or a story that's all about a little boy's quest to become the best at some adventurous profession but every now and then a quest comes along with some "mystery" involved or in the background well behind the core plot there are some unanswered questions. Yeah, when I put in the "mystery" genre I find myself very skeptical about a number of the popular choices.

Basically, I want something where a major point of the story, central or equal to central, is the task of finding the culprit in a crime or series of crimes. If at its core it's mostly just an adventure dealing with quests and monsters while occasionally there's some background unknowns, that's not it.

I haven't read any of the ones you mentioned so I wouldn't know how they fit. Nothing I've heard about the Apothecary Diaries made me think mystery or whodunit, so what in it constitutes "mystery"? Is there a big plot about finding a person who's done things or is currently doing things that need to be stopped?

Furitsumore sounds like a probable fit at least based on the description, though I could see it dropping the mystery fast given the emphasis on "shockwaves" through the department, like if the culprit is easily found but then tons of drama and problems arise because of who they are or who they're connected to (again, haven't read it).

No clue about Mitaraike, as there's really not enough info in the description. Theseus' Ship looks like a likely fit.

Perhaps you could give a description of the mysteries in those series, so I can get a better idea?

At the core, I want stuff where a big part of the story is centered around a "detective" (not necessarily in name but at least in actions) trying to work through evidence to try and identify the culprit or mastermind of some major incident. Also good are stories where someone is actively engaging or setting up preparations for some big crime. Supernatural abilities are fine, as long as it retains a large focus on finding the answers (for instance, in Kakeru where the guy has "heightened senses" that he uses to figure out what happened and who did it, or various psychic detective series where people get fragments of thoughts or visions of events and have to piece things together).
 

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