Shu

Hellooooo! ^__^
I'm (mostly) a piano composer, who has worked with a few VN creators before, and I'd like to share my music!
https://www.youtube.com/channel/UCAWCYLKjW6eHxGC0vHXq6pw
All music on my YouTube channel is original, and free to use for your non-commercial novels! Oh, and I'd really appreciate it if you give an attribution if you decide to use it!
If you have any questions, ask away! Thank you!

Inamuma Rio from Dracu-Riot would fit the description perfectly, I also think she had the best route in the vn.
 

Perhaps the most universal complaint of those who read Japanese VNs, regardless of their tastes, is the bland, non-people, average protagonists that make up better than 90% of all VN protagonists.  This trend began with the first moege, as a technique to allow people to self-insert more easily, but the tradition has worked against VNs more than it has worked for them, with protagonists with unique quirks turning out to be almost as important to a VN's lasting popularity as heroine quality. 
Unfortunately for those new to VNs, it is impossible to tell at a glance whether a protagonist will be interesting or not based on the cover, since most protagonists don't have a tachie, voice-acting, or a character description on the official site, lol. 
So, as a service to my fellow Fuwans, I decided to go ahead and make this list.  The greater majority of these games will be untranslated, but I will go ahead and list ones that are translated that I know of.  Feel free to help me add to the list, though this one is for Japanese-origin games, not EVNs. 
The baseline for these protagonists will be that they are either unique, unusual, or capable (intelligent, talented, and/or skilled at something and have something approaching a personality) without deliberate nerfing of their qualities to make heroines stand out more.  Harem protagonists who are merely kind to everyone will not count for the purpose of this list, and characters whose personality/capabilities/talents/skills get toned down in the heroine routes will also not qualify.
Translated
Tokyo Babel
Ayakashibito
Hello, Lady (soon)
Hapymaher
Noble Works (yes, he does make the baseline)
Dracu-riot (assuming the official release comes out)
Nanairo Reincarnation (soon)
Tsukihime
FSN
Comyu (yes, I include this... because even if you hate Akihito's man-whore qualities, he is definitely not a cardboard cut-out character)
Rance games (I hate the Rance games, personally, but you can't say he isn't unique)
Majikoi
Tsujidou-san no Jun'ai Road (Dai only seems sheeple on the surface... he has enough depth as a character to qualify) 
Eien no Aselia (while his personality is standard for a jrpg protagonist, it has enough twists and unique qualities to make the list)
Seinarukana (similar to above)
Fata Morgana no Yakata (I wavered because of the way the game is structured, but I chose to list it anyway)
Grisaia series
Kikokugai
Demonbane
11eyes
Rewrite (I hate this protagonist, but he stands out, even if he is a dumbass)
Animamundi
Baldr SkyDive (whenever it comes out)
ChuSinGura (I honestly wavered on this one, both because the protagonist is a moron and because I don't consider this to have been truly translated)
Cross Channel
Daiteikoku
Daitoshokan no Hitsujikai
Dies Irae
I/O
Yumina
Kyonyuu Fantasy (yes, I'm serious even as I'm laughing)
Planetarian
Rose Guns Days
Sekien no Inganock
Gakthun
Sharin no Kuni
Shikkoku no Sharnoth
Shin Koihime Musou (apparently tl is at 100%, so I'm including it)
Sorcery Jokers (Senri!!!)
Tears to Tiara
Tokeijikake no Leyline series
Venus Blood Frontier (whenever it comes out)
Wanko to Kurasou
Eden*
Untranslated
Akeiro Kaikitan
Ikusa Megami series
Soukoku no Arterial
Fuukan no Grasesta
Madou Koukaku
Silverio series
Tiny Dungeon series
Zero Infinity
Electro-Arms
Soranica Ele
Kikan Bakumatsu Ibun Last Cavalier
Komorebi no Nostalgica
Devils Devel Concept
Karenai Sekai to Owaru Hana
Evolimit
Bullet Butlers
Tokyo Necro
Soukou Akki Muramasa
Ou no Mimi ni wa Todokanai
Shugo no Tate series
Amatsutsumi
Floral Flowlove
Aoi Tori
Mirai Nostalgia
Bradyon Veda
Draculius
Gensou  no Avatar
Abyss Homicide Club
Hyper→Highspeed→Genius
Inochi no Spare
Hatsuru Koto Naki Mirai
Kitto, Sumiwataru Asairo yori mo
Konata yori Kanata Made
Kanojo wa Tenshi de Imouto de
Jingai Makyou
"Hello, World"
Natsu no Owari no Nirvana
Otome ga Tsumugu Koi no Canvas
Rui wa Tomo o Yobu
Ryuukishi Bloody Saga
Vermilion Bind of Blood
Satsukoi
Sinclient
Tenshi no Hane o Fumanaide
Suisei Ginka
Yurikago yori Tenshi Made
Izuna Zanshinken
Tasogare no Sinsemilla
Valkyrie Runabout
Sekai o Sukuu dake no Kantan na Oshigoto
Haru to Yuki
Semiramis no Tenbin
Tsukiakari Lunch
Tsuisou no Augment
Kamikaze Explorer
Prism Recollection
Houkago no Futekikakusha
Izayoi no Fortuna
Natsuzora no Perseus
Minamijuujisei Renka
Ojou-sama no Hanbun wa Ren'ai de Dekiteimasu
Yami to Hikari no Sanctuary
Sakura no Mori Dreamers
AstralAir no Shiroki Towa
Irotoridori no Sekai
Senren Banka
Reminiscence
Akagoei series
Soshite Hatsukoi ga Imouto ni Naru
Harumade Kururu
Haruru Minamo ni
Kin'iro Loveriche
Love Rec.
Natsuiro Recipe
Shuumatsu Shoujo Gensou Alicematic
Sakura Nikagetsu
Iroha ~Aki no Yuuhi ni Kagefumi o~
Campus's Uso series
World Election (seriously push this one for fantasy charage lovers)
Curio Dealer
Kami no Ue no Mahoutsukai
Lamunation
Sora no Tsukurikata
Hikoukigumo no Mukougawa
Sakura, Sakimashita
Amairo Islenauts
Blade x Bullet
Gouen no Soleil
Dekinai Watashi ga, Kurikaesu
Doushite, Sonna ni Kurokami ga Suki na no?! (more charage with some plot)
Boku ga Tenshi ni Natta Wake
Butterfly Seeker
Fake Azure Arcology
Re:Birth Colony
Gekkou no Carnevale
Hatsuyuki Sakura
Gurenka
Hikari no Umi no Apeiria (this guy's personality is so out there you wouldn't even be able to tell if anything effected him, lol)
Hotel. (this is also a joke from me that I can share only with those few who have read it, lol)
Kamigakari Cross Heart
Kimi to Boku to no Kishi no Hibi
Witch's Garden
Kono Sekai no Mukou de
Kouyoku no Soleil
Lovesick Puppies (more food for charagamers)
Toppara Zashiki Warashi no Hanashi
Naka no Hito Nado Inai
Natsuiro no Nostalgia
Ojou-sama wa Gokigen Naname
Onigokko
Otomimi Infinity
Para-Sol
Prima Stella
Paradise Lost
Kajiri Kamui Kagura
Sanzen Sekai Yuugi (only Otomege I know of that fulfills the prime condition)
Primal x Hearts
Tayutama  (original only)
Shinigami no Testament
Shogun-sama wa Otoshigoro
Stellula Eques Codex Tasogare no Himekishi (seriously, the protagonist is subject to some interesting stuff, like akuochi and/or corruption of characters)
Toki o Tsumugu Yakusoku
Unjou no Fairy Tale
Yuganda Uso no Koi to Letter
Yoru Meguru, Bokura no Maigo Kyoushitsu
Tsuki ni Yorisou, Otome no Sahou
Request includes
G-Senjou no Maou
Aiyoku no Eustia
Watashi no Real wa Juujitsu Shisugiteiru
Shirogane no Soleil
Root Double
Edit:  A lot of these characters stand out due to personality traits or quirks, as much as anything else.  The key point is that the protagonist is a 'person' instead of a cipher or catalyst.  For those who wonder why I didn't include Tsuki ni Yorisou, Otome no Sahou 2, the reason is pretty simple... in every path, the protagonist's individuality vanishes and he becomes enslaved to the heroine's character needs. 
 

I am already halfway through her route but couldn't stand her anymore.
Thanks.