Finally, after years I'm leaving my 2c here ;-). When the original elemental crystals were taken out of the battle shop, we were promised we'd be able to get PLENTY of them via other ways.

The means to get them is farming challengers beyond a (rather high) amount of wins. Pretty time consuming (and boring). You already need a fairly high statted pet to get Baguettes. If you have one battler only, you're on the losing end, anyway.

The mods are supposed to be swapped out. You lose the old ones. Granted, the lower tier ones are quite cheap in usershops. Still... The expensive higher tier ones I, quite honestly, don't want to "waste" putting them on weapons, that might need a different combo in the near future. (Also, there is a weird bug going round, where they don't work in special set ups/weapon combos)

Cut a long story short:

If you get 3 crystals out of 50 fights, that's just MEASLY!