One Piece: Madara Takes Over from the Start and Wipes Out the Buster Call

[Joins the crew early on, leaves in the middle (has left by now) + One or no heroine (the author is a Robin fan, so if there is a heroine, it'll definitely be Robin) + Ninjutsu + Anime crossover (the protagonist may summon other anime characters and acquire their skills). The protagonist isn't simulating anything; he just got Uchiha Madara's skills!]

Sluode transmigrated into the world of One Piece and gained a golden finger that lets him summon characters from other anime to possess him, granting him all their skills. But he must enter their world and fulfill their wishes once that world is over.

Uchiha Madara: “Kid, have you ever seen me in my prime?”

Aizen Sosuke: “Allow me to show you what true power is.”