Yeah, that's what people are afraid of. That, and that Capcom will sell DLC gems, giving people with money more access to better gems.
Capcom has said that they still haven't decided what they're going to do for distribution and all that, but they maintain that gems are all balanced against each other, so there won't be defined "best sets" for everyone or any overpowered gems.
We'll see how it works out in the end, i guess.
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XS2 is the only good Xenosaga game - Lady Ashe