Like in anime, movies, books, etc is the main character not the leader of some group of heroes. Rather he is a follower of a team and another character is the leader. But of course being the main character he plays an integral role.
Well I don't know any other manga like that, but in Naruto, Naruto wasn't considered the leader of Squad 7, Sasuke was.
lucifer and the biscuit hammer - the protagonist is the right hand man of the 'queen'.
7 seeds - the protag is...well, i dont know because theres multiple point of view here, however some pov does not involve the leader.
yugioh (i mean season 0 not the american one)
also soul eater is referring to asura for eating souls not soul evans
Claymore, Code Breaker, D Gray Man, Fairy Tail ......& the list will never end
The Melancholy of Haruhi Suzumiya. Kyon is the main character, and not the leader. Haruhi is the leader. and the villain. Watch or look it up for more information.
I'll even make it easy for you to look it up. Yay, me.
Well, according to that, Haruhi is the main character. But Kyon is the narrator, and I've always considered him to be the main character.