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At the moment it seems as though rare and legendary runestones are equal to common ones when trading them in at the tinker for mystery dust, given how many more levels are required and their increased rarity it seems a bit strange to me for it to be that way.

If they have an increased chance based on rarity at getting a high success level for blessing dust and a high destroy chance removal then fair enough, that'd be one of my suggestions.

Another would be to simply give two blessing dust for rare runestones and three for legendaries.

My final suggestion would be to give rare runestones a 1-7% chance of an increase in mystery dust rather than the usual 1-5% and legendaries to give 1-10%. That would probably include creating two items however.