A good point that many forget.
Each Prequel DVD is a two disc set. The "Original Trilogy" was a four disc set (3 movies + 1 bonus disc).
The new "Limited Edition" Original Original Trilogy movies will each be a two disc set, but minus the bonus disc.
So there will by the end of the year be a total of 13 Official Star Wars discs out there (I don't consider "The Stars of Star Wars" or similar specials to be official and I'm not counting the Ewoks/Droids or Clone Wars animated discs or the Ewok Adventures of course). 9 movie discs and 4 "extras" discs.
As far as a boxed set is concerned, yes, there really is nothing to be gained by waiting for a "boxed set" of all the movies, since the content would be identical as before. They'd just be a in bigger cardboard case. So I guess they might look nice on your mantlepiece having two big long boxes (of 3 movies each) or one giant long box containing all 6).
But for now, you'll have to create your own, or buy one from another fan.
I really am not a collector of DVD boxes. I only care about the movie discs themselves with the content I can watch.
As of now there is no benefit in waiting, though if you had yet to purchase a Star Wars DVD, this is great for you, because the 2006 limited edition set will be all you "need" (and then just order the "Bonus Disc 4" off of ebay or amazon and you've got all the content from all the previous sets released since 2004). The prequels haven't changed since they were originally released on DVD in 2001, 2002, and 2005 respectively.