For me, some red flags actually started happening after the time skip. While Sakura had a great fight in the first arc, I was rather disappointed that Naruto had barely developed and the only thing he really learned was how to make a bigger rasengan.
Even the fight with the wind rasengan was a bit lame for me since it was Naruto just trying to do the same attack a few times. The fight with Pain, though, was pretty good to start with, showing a lot of variety.
That was sort of a lone bright spot, I think. As the series got closer to the war arc, it started going more downhill. Then when the war actually showed up, it went completely off the rails for me.
The war, for example, all took place basically at once, in the middle of nowhere with a bunch of cannon fodder ninjas fighting reanimated dead. It got old so fast and there wasn't anything to latch onto in the action.
Then Naruto and Sasuke having god-like powers made it even more ridiculous. I always figured that the two would get to a really high level, but it went way too far.