Evolutionary stones are just there to make evolution easier (or harder?) to achieve. Like a permanent placeholder, if such a thing exists. It's simplistic at best, but I'd really like it if they, not replacing evolutionary methods, but developed a new way to use (or in this case, create) these, imo. Maybe through something like alchemy, perhaps? :p. Having to mix ingredients to create the finishing product, a stone capable of evolution.
I think that it's in the stone having some sort of futuristic property to them, a way of stimulating DNA evolution. The stone, coming in contact with the body, forces the genes in the Pokemon to mutate and evolve, giving them new strengths and appearances.