I agree with the OP - Having to augment the item in order to store it is extremely cumbersome. I have quite a few +2 pieces and only a handful are augmented because either the augment isn't very good or the job is just too difficult to take to Dynamis.

Perhaps giving us an alternative method of obtaining the augment would be a workable solution? Personally, I would rather turn in a bunch of junk items (think Kindred Crests, but only useful for a trial) that come from Dynamis rather than being forced to waste Dynamis runs by bringing in my COR just to augment.