I say just allow complete melding on both green and blue gear, even then crafted gear won't become useless for 1 reason:

Crafting gear is still far easier to come by than U/U stuff. People will be much more willing to attempt x2, x3, x4 or x5 melds on crafted gear than on U/U gear. There's no way I would risk a double meld on an Ifrit weapon for example.