* It got too hyperfocused around the Uchiha clan, especially Sasuke. This character always had very few redeeming qualities, and it's hard to buy him as Naruto's actual friend.
* Naruto himself was ruined. His original motivation to become Hokage took a backseat to saving Sasuke, who frankly isn't worth saving to begin with. Also, the revelation that he's a child of destiny totally ruined the "determination and hard work trumps all" message that the first part had. What was the point of his fight with Neji then?
* Too many interesting side characters were sidelined to focus more and more on Sasuke. Shikamaru was one of the few great characters who stuck around.
* The characters got too OP to the point that they didn't feel like ninjas anymore.
* The end of the Pain arc where he brought everybody back to life
There's more, but this is what really killed the series for me personally. There's the occasional dope fight here and there, and Kishi was smart enough to have Naruto wife Hinata in the end, which I give him points for. But overall, Shippuden is nowhere near the level of Part 1.
Jojo's, One Piece, DBZ, Fullmetal Alchemist >>>
EDIT: Hunter x Hunter is fire.