Since we're going to be getting stackable clusters, I'd like (and I'm pretty sure there are people who feel the same way, especially if they have a crystals-only mule) to see some way to recreate clusters from crystals.
Because of the limitations of the crafting system, it's obviously not going to be possible to make a synth - Synergy or otherwise - that does this, so here's my idea of how to handle this:
Add an NPC to the game who can accept crystals of any type, similar to Shami in Port Jeuno. You can retrieve individual crystals if necessary from this NPC, or, in exchange for reducing your stock of crystals by a certain amount (I'd lean towards 13, personally; while 12 means there's no loss of crystals in these exchanges, there are usually enough crystals generated that a small loss should be acceptable), you can obtain a cluster.
This method has the advantage of, well, being similar to Shami's existing system (only the numbers and specific items involved are different). I'm tempted to say some other things should be added (moving the HQ crystals out of the guild point system and making them cost two NQ crystals instead; possibly HQ clusters as well), but this would definitely work well enough as an method of decluttering inventory further.