Anyway on to Empire, the color corrections are looking really good, I honestly hadn't realized just how severe the color problems were, until seeing the side-by-side.
Here's my two cents on some other stuff:
Regarding the Wampa scene, I'm glad that you're losing most (if not all) of the Special Edition shots, however there's a shot in the original version that always bothered me... (I don't think anyone has mentioned this, apologies if this has already been discussed...)
We see a glimpse of white fur through a hole in the icy wall, and I swear it looks like it's on a dolly, it's rolling horizontally, with no vertical/diagonal motion at all. I'm sure you have noticed this as well.
I actually like the 3D fly-through stuff at Cloud City, as well as the CG windows, I wouldn't mind seeing those bits stay in.
I like the suggestion of shortening Luke's arm to reduce the obviousness that Mark's hand is still there, plus it seems feasible in terms of effects...
Otherwise I'm very comfortable with your general if-it-aint-broke approach.
OK that's it for now!