Prior to opening that thread, I actually thought people were bitching about HBO showing a cropped version of ROTS in HD.
Needless to say, I really like the movie. It's definitely flawed, but I don't really mind most of these points of contention that many of you bring up.
The thing I hated the most out of Revenge of the Sith is the opening sequence on board the ship. When I saw the film for the first time, there was something about the sequence that irked me. I couldn't really place it, but now I think it's R2's fault. Lucas's desire to put some more family-friendly material really slows down the sequence in the movie. While I was listening to the commentary, I was surprised that Rick McCallum actually fought to have all the R2 stuff removed. Unfortunately, Rick ends up saying something to the effect of "Good thing George kept it! He's a genius!"
I don't mind Hayden's acting at all. He seems to come from a different school of drama than we're usually used to. It's something I've also noticed in fellow actor James Franco (Harry in the Spidey films). They seem to come from a place that's more emotional. There's a level of amplified emotions in their performances. When they cry, they sob. It can seem more forced, but it's also rawer. I'm probably not explaining this well at all, but when I see Hayden delivering a line, it doesn't seem wrong to me. But perhaps I'm just more forgiving in the field of acting than others. I admire a great performance, but personally, all I look for is whether I can believe the actor in the part. When I see Hayden, he looks like Anakin. When I hear him speak, it fits the character.