OK, so I threw all of my BDs in and watched their bitrates and found something that likely relates to why some of the films aren't as good looking, and it wasn't simply MPEG2 that is to blame. I noticed that on promo material, they were using MPEG2, but at high bitrates and it looks quite impressive, for the movies that don't look quite as good, the bitrates are lower for video. For the ones that look good, they are pretty much up there at 30+Mbps while the less good looking ones average 20Mbps or less.
Grain was mentioned and I think that is more an artifact of the transfer as much as anything, who knows. These were some of the first films they did this with, so who knows what exactly the problems may have been. Now, with Sleepy Hollow, I see a LOT of grain also, though only in certain scenes, and I was wondering if this was some kind of artifacting from something that was done during the transfer or the processing that brought this out, because it seemed mainly on clearly digitally enhanced background scenes only. I also thought that maybe this is really just the fact that BD is actually a bit too good at showing the flaws of the film, sort of like when you have a great audio recording, you the flaws are far more glaring than if you didn't have such good recording/mastering. Just my .02