Foundation Imaging did a great job, but looking at the TNG Blu-Rays, I suspect CBS-D would be perfect for reproducing the work on the DE, as well as recompositing the original shots (assuming the original elements still exist independent of the movie).
Getting Darren Dochtorman, David C. Fein and Michael Mattesino et al consulting and working on the project would also ensure that they are doing it right for reproducing the VFX elements.
CBS-D would be able to work on the restoration of the original print, and the re-editing of the movie to match the DE DVD master (timing, sound mix etc.).
The issue with a project like this is money, more specifically, the lack of.
Paramount own the movie itself, and would need to be the ones behind such a restoration.
To do it right now would be bad timing, as it would take focus from Star Trek Into Darkness.
Not impossible, and I want it, but lnot likely in the short term.