Naruto would be nothing without Kyuubi
Gaara would be nothing without Shukaku
Shikamaru would be nothing without his high IQ
Neji would be nothing without his Byakugan
Itach/Sasukei would be nothing without their sharingan
Kakashi would be nothing...

a pattern perhaps?

How about, the characters are badass because of what they have, not because of what they'd be like without these things? Sounds good.

Actually, I agree that some characters do have an unfair advantage, such as Kyuubi and the Curse Seal, but whatever.