I don't buy the best of series for Pokemon either, but I'm still kind of surprised that they would continue releasing them. I could understand it during Pokemon's tenth anniversary, but I was hoping that they would get back to working on more of the older season box sets by now.
Like FireStarterLE mentioned earlier, there are already box sets for both Master Quest and Advance, but I don't think that you can find Master Quest in most stores. I did see an Advance set in a nearby Borders awhile back, but that could get harder to find over time. I think some places would still have single discs for Advance Battle and maybe Advance Challenge, but I agree that those seasons need box sets as well. Johto Journeys and Johto League Champions definitely need a release since I think those are the hardest seasons to find on video/DVRAB now.
I thought of that idea too when Viz announced the release dates for the Battle Dimension DVRAB. I agree that it is a possible theory and I would be seriously happy if that's what they're trying to do. A remake for G/S feels likely with all of the hints, especially with Pichu and the Johto starters in the next movie, so I'm hoping that that's what they're trying to do.