What didn't come across as convincing, especially in Sith, was the blue or green screen environments. The actors just never seemed to be a part of it ever. And it just stood out like a sore thumb. I really wish they had put much more effort into set building. In my opinion, TPM has the best effects of the prequel movies, having a nice enough balance of "old" and "new" technology, and it comes across as very believable for the most part. But to say that Lucas would prefer to do effects practically rather than with CG is just silly. Any number of recent interviews with him will prove otherwise.
I enjoy the prequels, I actually do. We're not all hating them for the sake of hating them. I just seriously don't think they're nearly as good as the original films. They have some good stuff in there, but it usually doesn't outweigh the bad, especially on Sith.