Let's look at it from Lucas's perspective. He prefers the SE, he doesn't feel like putting out 2 different editions of the movies in every boxset, he wants everyone to look at the saga as 6 movies, as long as the SE sell well in every release, why would he change? If the '04 DVD's were the #1 selling boxset that year, why should he think the majority of SW fans would want the OOT? Lets just say the SE + PT movies are released on BluRay in 2009 and it is the #1 selling boxset that year, why should Lucas not think the majority of fans want that?
Now if the SE + PT BluRay set does not sell well, then there Lucas & Co. will realize that the market may not want the SE movies, or care to rebuy the PT movies too. THEN he goes back to old faithful: OOT.
People have to speak with their wallet, and if this CloneWar movie does great boxoffice numbers, and the TV show gets great ratings, Lucas will move on and like he has always done: Go with the market that is lining his pockets in the PRESENT DAY.
Just think of all those SW'77 fans who don't recognize Vader as Lukes dad, or Luke & Leia as siblings, have they ever gotten a single release of Star Wars on VHS in that context? No, Lucas catered to the OT fans all through the 80's and 90's with Star Wars Trilogy Boxsets.