If Disney/Lucasfilm were smart/cool, they'd release Prequel "kits", with everything separated, and every shot, final cut or not. Hell, they could get crazy and release green screen alts as well. The best thing about the prequels, and Episode I in particular, is the fan edits. Part of the problem with the Phantom Menace is inherent, but another part is the imaginations of so many viewers. Fan edits allow people to at least inch it a little closer to what they wanted, and I think the powers that be should encourage this.
It's well past time to give up on the idea that TPM is equal to Episode IV, or whatever fiction Lucas, etc have been telling themselves. It's not a total failure, but it actually could be an inspiring success if they would open up the vaults for fans.