I wrote a small addon that goes along with the TradeNPC addon that will help you trade crystals to the Ephemeral Moogles with a simple command. It isn't terribly amazing, but saves a little time over having to open the trade window and select stacks of crystals.
It will scan your inventory for crystals and clusters and send a //tradenpc command that will trade exactly the number of items you have of each element.
If you have a plethora of crystals, running //ctr will trade all of your Fire Crystals and Fire Clusters in one go. After the trade, running //ctr again will then trade all of your Earth Crystals and Clusters in one go. It will let you know how many more times you need to run //ctr to remove all crystals from your inventory. I didn't play with sending {Enter} during the conversation with the moogle so you'll have to press it a few times and re-target the moggle for the next command.
GitHub