Several in this thread have pretty much nailed what's so bothersome about the prequels.

Lucas filled the original films with cgi so that when he made the prequels they would visually blend better with the OT, instead of leaving the originals alone and trying his best to make the prequels fit seamlessly with the OT. Moreover, it's a direct result of that philosophy that the OOT is now buried.

That said, I would love to see the theatrical prequels nicely preserved. Hell, I would think the new 2K scan of TPM could be the basis for such a preservation. Yeah, it's not a particularly good movie, but it was the second highest grossing movie of the 90's (here in the States, anyways). Likewise, the '97 SE of Star Wars should be preserved if for no other reason than its box office significance (still the highest grossing movie to open in January here in the States, AFAIK).