I was convinced Lucas was gonna eventually get around to it before any of this Disney business happened. The guy reversed himself on so many other subjects. Why would the OOT be an exception?
Now that Lucasfilm is part of a larger corporate entity, I'm all the more convinced it's gonna happen. The o-neg might not be the best starting point anymore, as skyjedi pointed out. Robert A. Harris should definitely be consulted on some level.
To me, they have two options to create a Blade Runner style ultimate set:
-They do a new scan of the o-neg. Right there, you've got the '97 version. They could then use this scan to do a "final cut" equivalent for the inevitable 3D/2D theatrical re-release. The tedious part would then be using the source scan as a basis for reconstructing the OOT.
-The other option is what they did for Blade Runner, using the new o-neg scan only as a basis for the final cut, meaning: color-time it however you want, cut it however you want, "fix" whatever you want. But I would sure hope this ends up the final revision of the movie, and I would think GL would want this as well. The guy won't be around forever, and considering how many times he's changed it I would think he'd want one last go at it before he literally can't anymore.
The '97 version could be scanned off the '97 IP. Assuming they don't ruin it with DNR, you'd have a nice transfer of how the SE's looked, restored colors and all.
The OOT could then be scanned from the best available source(s), be they IP's or seps. This is where Robert Harris' advice would really be useful.
Of course, there's no guarantee Disney won't just cheap out and continue to use the decade-old Lowry master (one that was really never good for theatrical exhibition), holding it up as the best the films will ever look, a "digital negative," et cetera. I'm probably letting the fact that the Indiana Jones movies got new scans get my hopes up when it comes to Star Wars. Hell, even Willow got a brand new transfer for its blu-ray release.