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My ultimate box set would be separate 3-disc versions of each film, with one disc containing the original cut, one disc containing the final Special Edition cut, and the final disc containing all the special features. This would allow maximum bitrate for the best A/V quality and keep the presentation very clean. It would also allow them to break up the set into indivdual 2-disc releases very easily, like a 2-disc original cut and a 2-disc Special Edition.
Most definitely. I would be perfectly happy to go out and buy a 9 disc trilogy Ultimate Edition. However, I don't think seamless branching should be entirely ruled out. It would mostly be a matter of having a higher number of chapter stops than usual, and the length of the OT and SE trilogy is such that bit rate would not be severely compromised. Anyone who doubts this should take a look @ the Beauty & the Beast Platinum Edition, which crammed 3 different versions of a 90 minute animated film onto one dual layer disc, and it looks very nice indeed. Just a thought.