I wouldn't mind Kabuto so much if he was built up as a legitimate threat rather than Orochimaru 2.0. I thought he was supposed to be some kind of conflicted character at first considering he did try to murder Sasuke, Orochimaru's future body. Then, the dude fights Tsunade, one of the legendary Sannin, and was doing alright for the most part. Then Naruto rasenganed him in the stomach, and it all went downhill from there. We don't see him fight or do anything worthwhile for, well the rest of the story. Then he gets Orochimaru inside of him and suddenly we're supposed to care again? Nay sir, not when we have shark-people and giant venus-flytrap men waiting in the wings.
As for the whole 'ninja' issue, I like to think of it more as a title rather than what they are. They're not ninjas, nor are they vikings or pirates. Ninja just seems like the closest label since they jump around in trees alot, something vikings or pirates do very little of.