You can buy revives and you can farm infinite heart scales once you have the good rod and access to Chrisolia forest. When mining, you should focus on getting the fossils, one each (Helix, dome, root, claw, skull and armor) since they are the only way of getting those six pokemon. The Helix fosil is especially important because you will need it in a future to unlock some sidequests where you end up getting the gen six fossils. Appart from that, you should try to get an odd keystone, which you need to get Spiritomb.
Plates can be useful if you don't have anything else to attach to your pokemon, or if you want them for collection purposes. Shards are quite important in order to use the move tutors and the pokemon black market, and they are really expensive if you want to buy them, so getting shards is never a bad idea.
Finally, I would strongly recommend not to mine some rocks and to remember where they are, so that should you ever need an evolutionary stoon and you've used all of the available ones you can get another. For example, suppose you need a third moon stone. The only way of getting it right now is through mining.