It's been a while since I read HP, but there is /no/ comparison between Harry's growth and Eragon's. Harry is shown as flawed, beatable, and definitely not all-powerful. And he never, ever, /even by the end of the series/, surpassed Dumbledore. His friends aren't Team Canon Fodder, but he doesn't rely on them for everything either. And Harry suffers far more defeats and even humiliations than Eragon, but he still rises up to do /the right thing/; the willingness to deliver justice is far more important to a hero than having kickbutt, godmoddy dragonrider skills. Anyhow, I can go on and on, but this thread isn't about HP.
Yes, "main character beats everyone" is rather common. Doesn't mean it's right though. I have said that "Eragon is popular for a reason" right? So yes, it does surpass many other works. But "main character beats everyone" is still a problem. I object to it whether it's in Eragon or any other book, so I can say with a clear conscience that I'm not being unreasonable or biased.
However, "killing everyone in sight" is /not/ common. Unless it's a world half empty and you have to do it to survive, or if you have a villain protagonist or a Byronic hero. And note that, when anti-heroes go on killing sprees, they get called out for it, big time. By both the author, audience, and /other characters/. When a character kills many and experiences no consequences, you bet the readers are going to complain no matter which book it happens in.
But I have to disagree with Khalim in that Eragon isn't flawed. He is. "C" just doesn't realize it. =P