Lack of prominent women/women don't get to do anything
The current power level is ridiculous, like the third Raikage who could battle 10.000 people himself, calling down meteors from the sky and so forth. Not to mention that some people are just simply...forgotten. Like the Fodder 11
The fact that you can apparently steal DNA to make yourself stronger
The Sharingan. It was awesome at first but it became ludicrous in Shippuden with what it was capable of. And that it is able to evolve into the Rinnegan was the hair that broke the camel's back for me.
Again for emphasis - Many awesome characters are forgotten.
Sasuke going from an awesome character to an obnoxious little brat.
Kabuto.
Edit: forgot the most important part - Jinchuriki. I absolutely loathe how there are more than Gaara and Naruto. Not to mention that they were apparently part of some kind of peace argeement. I don't know, I just don't like the whole "becoming friends with your Tailed Beast" and that nonsense.
Also, it makes Naruto and Gaara far less special. It could've been done so much better, like just adding Bee instead of a whole bunch of others.
Last but not least - They can be controlled with the Sharingan. What utter bullcrap.