Here are my thoughts:
As for the Inception collection of pictures, the VC-1 is superior. The reason is because all of the other shots show vignetting in the corner of the frames! It's pretty clear that they zoomed in to cover that. As for encode quality, the only one that matches the VC-1 encode from a technical standpoint is the "Blu-ray promo (Warner 2011)" and even then it's a toss up. It looks slightly smoother and has some small blocking in the bricks whereas the VC-1 encode looks like it has a "coarser" quantization with more grain like elements to the picture. The other AVC encodes show obvious, if not significant, artifacting.
The Matrix pictures are bad, no bones about it. I've been very vocal about my dissatisfaction with the color timing changes to the film, so I won't get into that here. The existing masters are terrible, with significant horizontal aliasing everywhere. Even the new master is pretty soft, likely scanned on something like a Spirit Datacine. For one of Warner's VC-1 encodes, the artifacts are pretty minimal and likely have low perceptibility in motion (at least in that scene/shot).