1) Shorten up the OT disc. Definitely. ESPECIALLY Leia's theme, as that is hardly in the movies, or at least not as recognizable as other themes, yet it's about 4 minutes long (in other words, too long). Other things could be trimmed quite a bit, too. I agree with you in that since the PT soundtrack isn't as instantly recognizable, it's easier to play with and not get your head chopped of because, God forbid, you don't have the complete Imperial March! (Also, I'd shorten the March up a bit as well).
2) Make the PT disc end with less of a finality. While it works in the sense that its the end of a first act of a two-act play, if you listen to them all at once its as if it's over and then - whoops! - another hour and 20 minutes is left. I'd make it transition into Leia's Theme more, then split the discs. You could always have an artificial dissolve for people who would burn this onto 2 CDs rather than listen to it continuously on the ocmputer.
3) Smooth up some of the rougher transitions.
And that's about all I can think of for the time being. Other than that, excellent project!