It's not impossible for the CG to blend in with everything else, but it would have to be damnably difficult. Troy and the Lord of the Rings movies had some of the least oppressive CG that I've ever seen. You knew that the tens of thousands of soldiers were fake, but they added so much to the film and didn't act like they didn't belong. As for Attack of the Clones, there was always something cartoonish to me about the Geonosis battle, though I didn't know the extent of the CGI until George Lucas bragged in his DVD commentary about how he only had six clone trooper uniforms made for the movie. That doesn't seem like something to boast about, in my opinion.
CG can be a useful tool, but it can also be a hindrance. Filmmakers can learn to rely upon it too much, and it completely distracts from the story when that happens.

As for stupidest prequel complaint: it would have to be 'God, Jar-Jar! What the f*** was Lucas thinking?' Though many would disagree (and that's totally okay with me), I actually don't mind Jar-Jar, for my part. But that's just me.