I would be content if they at least put out the oldest and newest/final versions in equal home video quality.
That said, I think it would be really cool if they included all of the theatrically released versions. This would basically mean the 77/81, 97 and final versions for Star Wars; the 80, 97 and final versions for TESB; and the 83, 97 and final versions of ROTJ. They would have to do three-disc sets for each movie, since none of the three versions could really be branched with each other. They could get someone like RAH to restore the older versions and he could use the OUT and 97 IP's as a starting point.
For Star Wars '77, they could still presumably use that technicolor separation master we've heard so much about. That, along with the '77 IP, would provide a pretty good reference.
The '04 version is what I think will end up as the "lost version" most likely. If they do indeed put out the movies theatrically in 3D in the year 20xx, I think it'll probably have some additional (and probably minor) alterations from the '04 version. Hey, if people really end up wanting a preservation of the '04 version, they can come right to this very website for information!
As for the prequels, well, I can't imagine Lucas would alter AOTC and ROTS. Digital Yoda in TPM is a given, but that's about it. I would really hope that he includes the original version though, since it's one of the highest grossing theatrical releases of all time. I can't help but think GL made that longer dvd cut to distance himself in some way from the summer of '99 and all the negative reactions.
If they really wanted to go all out they could branch in the 35mm versions on the AOTC and ROTS discs, or even the AOTC IMAX edit, but I'd settle for the versions we have. Just give me the theatrical TPM and I'm happy.