To speak directly to the obtaining of crystals/shards, Foxclon was able to speak to Yoshida and the development team about alternate methods of acquiring crystals/shards after the removal of elemental point allotment in patch 1.19.

By equipping gear with elements, crystals/shards of that element will appear more frequently, so once elemental bonuses are removed, crystals/shards can be acquired through experimenting with gear. Players can also equip accessories with elements, and by using the materia craft system in patch 1.19 they will be able to attach elemental materia to weapons and armor.

So you can still obtain crystals/shards with the elements of your choice after patch 1.19. I will also forward your questions regarding elemental affinity after patch 1.19 and I will be back when I receive an answer!