In my personal opinion, desert stones are the worst boss drop in the entire game. For solo play, desert stones are completely worthless. When playing with other people, desert stones are more useful, but you still don't ever need the amount of desert stones you get. You will never need 30 desert stones ever. If Antlion dropped only 1-2 desert stones, that would be significantly better. Klaus also should not drop desert stones. But anyways, I'm getting a bit off track from the point of this thread.
I think an excellent way to fix Desert Stones and make them useful for everyone is to make Orange Gems attainable via Desert Stones. According to Maxwell, a Desert Stone is just "An impure orange gem." So, perhaps the Shadow Manipulator could unlock the recipe for Orange Gems in the Refine tab, costing 1 desert stone for 1 orange gem. Another possible way to make Orange Gems attainable from Desert Stones could be mining the stones, to get the gem that is buried in the stone out. (if you don't know what i'm talking about, the desert stone appears to be an orange gem that has been coated in sandrock.)
Anyways, I hope it wasn't too hard to get through my ranting about desert stones, but I really think this would be a great change to them.