@Anzor
Alright, I was too tired yesterday. but I found a few, and like I said there aren't many puppet masters like Light Yagami (Death Note or Lelouch (Code Geass) out there, unfortunately.
Most People just really never get tired of the same old tropes, look up: Idiot Hero, All-Loving Hero, Socially-Awkward Hero, and Chaste Hero on TV tropes, they're goddamn everywhere.
So these are the ones with straight up manipulative protagonists that I liked:
https://mangadex.org/title/1275/lost-brain (Uses Hypnosis to control society)
https://mangadex.org/title/21758/kaifuku-jutsushi-no-yarinaoshi (uses some insanely versatile healing magic to get revenge and builds a harem along the way)
https://mangadex.org/title/15438/maou-no-hajimekata-the-comic (old mage finds an endless source of mana, gets eternal youth, builds a dungeon, brainwashed harem, conquers stuff)
https://mangadex.org/title/15417/himekishi-ga-classmate (builds a harem with slave magic, the women actually enjoy it, don't ask me how that works.)
https://mangadex.org/title/21877/meikyuu-black-company (Guy who got lucky with stock trading goes to another world, ends up working in a mine, schemes for profit, hilarity ensues)
Here are some cunning/smart protagonists that I liked:
https://mangadex.org/title/617/aiki (created his own martial arts style, crippled by his father to keep him in line, lives a life of hedonism, some female apprentices show up, fun times)
https://mangadex.org/title/1230/black-lagoon (Office worker becomes a tactician for modern pirates/mercs, hot chicks with guns, badass anime adaption(subs), I also recommend Jormungund)
https://www.webtoons.com/en/fantasy/the-gamer/list?title_no=88 (Highschooler, gets an RPG system, becomes a pure mage protagonist in modern Korea, my favorite non-adult webcomic)
Here's some fiction/LNs with evil manipulative protagonists that I also really liked:
https://www.novelupdates.com/series/dungeon-defense/ (Korean dude reincarnates into the body of a demon lord from his video game, decides to conquer the world to save it)
https://www.novelupdates.com/series/ouroboros-record-circus-of-oubeniel/ (reincarnates, is irrationally afraid of death to the point of insanity, becomes an alchemist to obtain immortality)
https://www.novelupdates.com/series/warlock-of-the-magus-world/ (The most selfish, evil, benefits first Xianxia MC I've ever seen, and I absolutely love him for it, 10/10 IMO)
https://www.royalroad.com/profile/26619/fictions (Anything written by this dude is pretty much an evil or amoral MC making a slave harem while conquering something, 18+ warning)
https://www.royalroad.com/fiction/5812/euphoria (This one is basically madness, evil psychopathic MC, no holds barred, people are either in love with it, disgusted by it, or just don't get it)
And that is my list of evil, cunning, and/or clever MCs, I may have others, but I can't remember them at the moment, hope you like them.