Yeah, I agree. I found the same issues the last time I did a 5D project, I had the same issue and got around it using plain old 442. But that was before the Canon plugin made life easier. It was converted using MPEG Streamclip, a method that always made me ponder regarding quality. I dont know why, something just didn’t ring right about it. The fact that it interlaced my progressive footage even when I asked it not to made me question its ability to output quality footage.
However, this is the first time I have done a 5D project since the release of the plugin. So I brought a clip in at 4444, did some grading on it and it graded much better than the last time. So I went with it, not caring about the size of the files I was creating. However, it was shot better and I have more grading experience under my belt now so that could also be a contributing factor. But based on that grade I went ahead and imported it all as 4444, that was probably a bad decision (because of bloated files if nothing else). I am going to fetch a dark clip in at 4444, HQ, LT and plain old 442 and do a side by side by side by side test on the lot. I am most certainly not saying you are wrong, in fact I believe you are right, its just nice to see with my own eyes. plus I can post the results and hopefully prevent others from creating bloated files and actually decreasing quality.
As it stands