I'm not sure if I can explain this well, but I'll try my best. 🤢 I am looking for a manga that has more to the plot than just the romance. For example, they could be detectives or some sort of supernatural being (demon, angel, psychic, etc.). It doesn't have to be long. It can be either shounen-ai or yaoi. It can even be hinted yaoi, but it must be pretty noticeable (like in Wild Adapter, Komatta Toki ni wa Hoshi ni Kike! and Kuroshitsuji).

Here's some to get started. These are all more plot-heavy than most yaoi.
My Life with You
Crystal Harem
FAKE
Mezase Hero!
Totally Captivated
Bi no Isu
Nightmare Fortress - Majin no Jousai
Vassalord - shounen-ai, but very graphic shounen-ai 😉
Tengoku e Ikebaii
Crimson Spell
Un Carnet de Bal - historical
Wild Rock - prehistorical

For supernatural you can't beat NAONO Bohra. Maybe try Three Wolves Mountain

These are mostly shounen-ai:
From Eroica with Love
Banana Fish
Earthian
From Dusk till Dawn
Gohou Drug
Blood+ - City of the Night Walkers
Koori no Mamono no Monogatari
Silver Diamond

Maybe....

Toukaidou Hisame and the sequel Toukaidou Hisame - Kagerou
Yasashii Ryuu no Koroshikata
Madness
Macaroni

Lets see.... The ones I listed below are ones that I thought had a very obvious plot other than the normal cut and dry Yaoi. Hopefully some of these fit!

Calling - they are training for a police type job and then end up being secret agents (not finished but really good)
Crimson Spell - very well known and you have probably already read it but it is fantasy
Ai ga Kami wo Korosu Toki - plot set in New York City - Mafia related
Akuma no Himitsu - fantasy related with an Incubus
Cut - a lot of angst so it is definitely not your cut and dry romance yaoi
Dear Myself - Amnesia (really great manga)
Itsuka Koi ga Kanau Made - I think this kinda fits... maybe not >.<
Izanai: Hyakunen no Koi - This is a oneshot about a vampire
Keep Out (KISARAGI Hirotaka) - Bodyguard
Hero Heel - TV Actors
Kiss Me Princess - Manhwa about a prince - a lot going on here
Koisuru Cupid - I was a little reluctant to put this one on here but it's really good and has a ghost in it ^.^
Koyoi wa Kimi to Chi no Kiss o - This is about 3 vampire brothers
Little Butterfly - really great story and has a psychological feel
Lovers Doll - really cute ^.^
Mister Mermaid - supernatural..... as you can guess it is about a mermaid... er man.... art is old style but it is a good heart wrenching story
My Life with You - Military
Nekrateholic - Vampire ^.^
Nemureru Hana - really good (Warning: contains rape)
Nemureru Tsuki - HIGHLY recommended!!! One of my favorites!
Ore no Tenshi wa Mayonaka Akuma - really cute and different
Pathos - my personal favorite vampire Yaoi
Replicant no Kiss - Sci-fi
Sakura-Gari - A lot going on in this manga... a must read if you haven't read it already (Warning: contains rape)
Machina Angelus - I haven't read this one but it is on my wish list. I am sure this one would definately fit.
Take Over Zone - this one has a sports theme to it - I normally don't like sports manga but I really liked this one
Onigari no Mori de - really good (Not finished but it is still being scanned and updated)
Tenshi no Uta (NISHIDA Higashi) - Full of angst and really good
Totally Captivated - this is my favorite yaoi manga - I am sure you have read it but it is mainly about the Korean Mafia
Toxic (MIYAMOTO Kano) - Shounen Ai oneshot. Supernatural
Tsuki ni Hoero - Werewolves
Uchi no Tantei Shirimasen ka? - Private Detective
Wild Fangs - a really good vampire yaoi also has sequel Wild Rose and Wild Wind
Yokan - it is about a Visual Kei JRock bank (Well they dress like visual kei....) Really good though
Yume wo Miru Hima mo Nai - studying to be airplane pilots
Acid Flower - about a special race of vampire - very explicit - unfortunately this isn't finished and has been dropped by the mangaka >.<
Kuuchuu Teien - Maybe.... meh... Yeah I think it will fit (about a prince)
1001 Nights - great Shounen-Ai
Corsair - Pirate

There.... now, hopefully a few of these will be of help to you (Sorry it was so long)
I started working on this list before there were any posted so I do apologize if I double listed some that Scarlet and Sorania posted - but hey if they are double posted, they must be good... RIGHT?? ^.^

Quote from xXGazeChicXx

...
I started working on this list before there were any posted so I do apologize if I double listed some that Scarlet and Sorania posted - but hey if they are double posted, they must be good... RIGHT?? ^.^

That is right! But amazingly there were just a few duplications. Some on your list I would have suggested if I had remembered them.

I second all the MIYAMOTO Kano suggestions, though I didn't post any myself. Haven't read Calling yet, have to something for a rainy day. 🙄

I feel like I have to say this: Thank you scarletrhodelia, Sorania and xXGazeChicXx. So many recommendations! I love this topic

Quote from xXGazeChicXx

I started working on this list before there were any posted so I do apologize if I double listed some that Scarlet and Sorania posted - but hey if they are double posted, they must be good... RIGHT?? ^.^

Haha I can understand why Scarlet and Sorania had enough time to post before you did.... Your list is amazingly long! Thank you so much!

P.S. Double posts definitely give me a good impression!

Quote from regnum

I feel like I have to say this: Thank you scarletrhodelia, Sorania and xXGazeChicXx. So many recommendations! I love this topic

I agree with you! They have so many recommendations! 😃 Thank you for all the great manga!! I haven't read most of those manga and I have a pretty long yaoi list, if I do say so myself! 😀

And "Yellow" by Tateno Makoto. And Fake by Matoh Sanami. Both good detective mangas.
I will also mention La Esperanca. That was a bit mysterious.

Thank you, great one, who was so kind as to consolidate my posts. I love you. 🙂

Quote from KuroBara103

Quote from regnum

I feel like I have to say this: Thank you scarletrhodelia, Sorania and xXGazeChicXx. So many recommendations! I love this topic

I agree with you! They have so many recommendations! 😃 Thank you for all the great manga!! I haven't read most of those manga and I have a pretty long yaoi list, if I do say so myself! 😀

I am glad that the recommendations were of help to you both!! 😀

Koujitsusei no Tobira - lots of spy/mystery intrigue
Saezuru Tori wa Habatakanai - yazuka, also BEYOND EXCELLENT
Hyakujitsu no Bara - historical war setting, though lots of smut lol
Yuuutsu na Asa - taishou era, focuses a lot on the couple but the plot often gets in the way~
Life, Love - kidnapping and gangsters in the U.S. not many chapters out though ;_;
Hari no Hana - historical, still ongoing
Acid Town - more mobsters

;D