Something like Skyfire Magus on RRL, he keeps on having these people inhabit his soul. It's always funny to see some guy talking to someone inside him who almost always judges him for his life choices. I really don't like harem and I don't the gender of the MC except no genderbender.
I would recommend Sevens because it is just plain hilarious, but you might not like it since it does have a harem that just keeps getting bigger and bigger...though seeing the mc cope with it is also part of the fun
+1 for Isekai Tensei Souduki. It's hilarious since he have 3 soul in his body. An old man, a high school boy, and original soul.
The harem in Sevens shouldn`t be an issue, the way it is executed diverts from many novels. If Sevens said it had the second best harem in novels, no other novel would dare declare itself first. Well, maybe Mushoku Tensei.
Akuyaku Reijo Ni Koi Wo Shite The Crimson Dragon(more hybrid human dragon) The Nine Godheads(many soul grampa) After Transformation, Mine and Her Wild Fantasy(1 soul 2 body but execution is not that great)
Martial Emperor Reborn He transmigrated, but the previous soul didnt die. Complete with brainwashing other people.... If you are looking for a dark novel, it cant get darker than this...
Volatile evolution on RRL (which I actually just rediscovered by reading your request, somehow was deleted from my list)
Not exactly a soul in his body, but something similar happens with the MC of the house of blades. He carries around doll that are his advisers and talk to him telepathically. He can also talk to them in this way, yet sometimes talks out loud earning himself a couple of ackward stares. "Because I`ve got nothing better to do", Simon thought sarcastically, but there was no doll around to appreciate it.
I'm conflicted because if I recommend the novel I'm thinking about, it'll spoil it. Like, the biggest spoiler. XD