My choice would be either the above, full 6 movie set, each movie having both theatrical and SE versions on it. I wont even go into bonus discs as this gets crazy (disc for each movie, each trilogy, whole saga, it would get quite big)
or the other way i would go would be like what Gaffer Tape said. I would have released a collectors set instead of the bear bones re-release (think 3 and 4 combined). Since its a collectors set you could probably charge more for it. I would have it as the original movies, unaltered in all respects except to be cleaned up to represent what was shown theatrically. Then there would also be (side 2?) a version that is still the OOT but has all the Matte lines and other effects cleaned up.
there are so many options he could do because there is so much material to release. The ultimate set would be like the to do something along the lines of the Ultimate matrix set. if this was done for all 6 movies it would be huge, as that was a 10 disc set that had each movie, an extra disc for each movie, an overall extra disc (i think), the animatrix, and a few other discs. But a prequal set and ot set could be released and the boxes could have stand alone images that when put together make a saga image. and even make a box sleeve available by mail with proofs of purchase if you buy the OT and PT. man, im not even in marketing\sales and i could go crazy with all the possibilities.
-Darth Simon