This is a topic that comes up with some frequency both internally and externally. We have plans for a future patch that will introduce more uses for any gem you have excess of as well as a way to increase your ability to get specific gems that you are lacking *read Topaz*.
As a general philosophy point, anytime we introduce mechanics that are intended to consume limited resources this is something that players will encounter. Whether it's gold, gems, or a specific crafting material, these are all meant to be gathered and consumed at varying rates. Inevitably, and intentionally, there will be times when you need more of some material than you have. The problem isn't that you are running out, the problem is when there is no mechanism for you to alter your gameplay to gather more of the thing you need. When you run out of blue material you start picking up blue items you were ignoring before, when you run out of gold you equip your Boon of the Hoarder if you've found one etc. The problem isn't that people are running low on Topaz from enchanting, the problem is that you have no way to increase the rate of Topaz you find when you want to. This is what we will be addressing in the future.
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