It seems you like that genre of shonen so I'd recommend either Soul Eater or Full Metal Alchemist to you.
Soul Eater is actually pretty unique in that fact that there's possibly three sets of main characters. Maka and Soul are recognized as the main ones I believe but it would be hard to tell. The idea is that this ancient and powerful entity named Shinigami set up a school. Fighters are either a tactician (a weapon user) or somebody who can transform into weapons. If they're compatible with each other, they will obviously be more powerful. Oh, and the weapons can eat souls. After 100 souls, they'll transform into an even greater weapon. They get these souls from defeating evil figures and what not. As for the enemy, I guess the equivalent of Naruto's "Juubi" would be Asura but there are plenty of other villains along the way.
Full Metal Alchemist is another alternative. These "alchemists" can have a variety of powers. As for the main characters, Ed and Al, they're trying to gain back the body parts they lost after attempting a certain forbidden ritual. The first few chapters might make people wonder what's going on but it clears up later. It's a pretty great series.
