I'm not sure about making single crystals stack to 99... this idea has been mentioned in the past and (if I recall) SE was not interested in doing this for some reason. Might be the disjoint between clusters breaking to 12, and stacks being not 12, I don't know. I just recall it being brought up and rejected a few times in the past (and no, I have no sources to quote other than my own memory, sorry.)

As for reforming crystals into clusters, I would be all for that, now that they will be stackable. Something that could be done on-the-fly would be ideal (as in, out in the field, not requiring an NPC or some such). When out leveling jobs and such, having to toss crystals that I'm getting due to inventory space is kinda silly, knowing that I'm just going to have to buy some at the AH next time I want to craft. Being able to "squish" them back into stackable clusters would indeed be awesome.