As an addendum, perhaps recompositing some of the effects shots digitally to clean up the matte lines, and get more clarity out of the model elements (compositing elements in 1979 produced some generational degredation whenever a layer was composited in to produce the effects).
I think that would go against the spirit of the DE. That project was treated as an act of film restoration; the goal was to make the new shots look the way they would've looked if they'd been done in 1979 using the techniques available at the time. So the CG was "downgraded" in certain ways -- animation elements were done 2-dimensionally at 12 fps
, film grain from the authentic period stock was scanned and superimposed on the digital shots, etc. They were trying to preserve and replicate the imperfections of 1979 film technology, not erase them.
I've heard this again and again, but nobody I've ever talked with who worked on feature fx in the 70s was shooting animation on 2s ... for TV, yeah, but not high-budget features. I've interviewed more than 30 vfx guys from TMP in the last 20 years, some still in the industry, a few long gone from it, and even if their recollections differ on details, nobody has ever even implied that a shooting-on-2s situation ever arose on TMP. Plus if they were trying to match the look of late 70s ship footage, they'd've been better off animating high-quality stills of the model, which would have had more detail than the CG ship (that is how the still cutout work in 2001 worked so well -- it was done with Hasseblad cameras that produced quality far above what could be detected even with 65mm film cameras ... I used to own a 16x20 still of the TMP ship that must have been shot using a 4x5 or 8x10 camera, because detail wise it was like looking through a window at the model.)
REGARDING THE DIGITAL RECOMPOSITING IDEA ...
Also, although digital recomping would be ideal (and was suggested on this board a couple years before the TMP DE even came out), it is almost certainly impossible because Paramount doesn't have many (or any) of the pre-comp elements. They were pretty much abandoned at Apogee and EEG after the film was done, and while i haven't heard about what happened at Apogee, am pretty sure EEG threw them out in 1982 when they had storage issues and were tired of waiting for Paramount to come get them. Then again, this is in keeping with Brick Price seeing one of the newer spacesuits (one actually used in the release cut of TMP) in a dumpster before the film even came out.
Contrast that with Ridley Scott paying to have all the BR VFX elements stored in ideal conditions in 1982 and for the next quarter-century, and it gives you an idea of how Paramount has kept their eye on the future with respect to Trek ... mostly with the eye that has a patch nailed over it.