That's not some easy requirements you're giving out but I'll mention the VNs I have read where the protagonist is somewhat realistic in the sense of personality but I won't stay away from unrealistic stories since you didn't mention anything about that. Someone will probably correct me is i'm wrong as my memory isn't the best.
Ayakashibito the story is unrealistic with powers involved, the mc might be somewhat unjustified op but he still has a hard time against his enemies, it's a good VN but it has alot of h-scenes and some tags that may turn some people away. He's mature and he has none of the personality traits you mentioned but perhaps dense, I can't recall wether or not he was dense, he wasn't unbeliavable so since I can't recall atleast.
Grisaia no Kajitsu you said you didn't wanna read grisaia because you've watched it on anime but i'll still recommend it as the VN is, in my opinon, alot better, the VN sususally are.
Sharin no Kuni Himawari no Shoujo allready been a few recommendations for this one and ill so again, it's a good VN with a good MC, he's not dense as far as I rememeber and not perverted at all, he's mature and he's a high school student.
Symphonic Rain a good VN with a avarage personality protagonist, mature and not op in any sense compared to the three above. The gameplay in this VN is optional so don't let that scare you away.