Well to be honest, the material on any one of the Prequel bonus discs utterly puts the Original Trilogy one to shame. In fact, much of the stuff on the OT one wasn't even about the OT! (The video game commercials and the Episode III teaser fluff).
Missing out on the Prequel bonus discs would be missing a lot.
Like I said, I've seen the Bonus disc by itself for sale on amazon, and ebay. So you don't need to buy the four disc set or wait for a big set to hypothetically come out in the future to buy it.
There's a fan selling custom made (and quite cool) boxes for DVD's (just empty boxes to put your keep cases inside), but unfortunately the Star Wars one (which is HUGE and large enough to fit all the official DVD's released thus far inside, iirc) is quite expensive, approaching 100$ but I don't remember the exact figure. Considering that the official "giant empty box" you could buy from New Line to put all your EE LotR sets inside was less than a few dollars, that seems excessive.
Then you realize it's just one guy doing it out of his home, and it makes more sense. But still!
Making your own would probably be the cheapest solution. Buy the discs piecemeal and get Kinkos or Copyworks to do it for $15 or whatever it would cost. You can download artwork virtually ready to go as well and just tell them what you want.
I wonder how many people will sell their old sets in time for the new one?