These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crosses the Line Twice: Many cruel jokes become even funnier because they are being repeated again and again, with increasing levels of ridiculousness (like Sasuke being gelded and blinded by Gaara, with increasing amount of female Naruto clones cheering on him each time, while real Naruto makes even better picnic for Kankuro and Temari each time, or Hinata sealing the whole main family with caged bird seals).
It also crosses the line thrice in one case, with jokes on Sakura becoming funny, and then sad again when you start feeling sorry for her.
God-Mode Sue: Given that he can both use shadow clones and is stuck in an infinite loop, this quickly becomes apparent.
Also, given the author...
Ron the Death Eater: Team 7 in spades. The worst offenders are Kakashi killing Naruto for embarrassing Sasuke, Ino getting into Sasuke's mind and finding out he has no redeeming qualities at all and Sakura (before her "redemption") agreeing with whatever Sasuke does or says and being an extraordinary bitch to Naruto.
The Sharingan itself is apparently malevolent. When Naruto uses it and looks at something to complicated for the Sharingan to decipher, it hijacks the rest of his brain in an attempt to understand.
Strawman Has a Point: When Naruto insists he's not interested in Sakura anymore, he claims that if she was genuinely interested in him she would have accepted one of his date offers. The problem is, by his count Naruto asked her out thousands of times over four years. Even if Sakura had thought of him as a friend, being asked on a date multiple times a day (on average) doesn't mean he's persistant or genuine about his feelings. It means Sakura needed a restraining order against him.
Sakura actually demonstrates several cases of obvious concern for Naruto in the early chapters that put the lie to much of the author's assertions about her; even when the author is working to sustain the premise he can't resist undermining himself by having Sakura bash herself because she cares about Naruto.