Well I was thinking about this today, Not sure if it's been suggested before or not.
Weapons/Misc Training
Basically when you acquire a cert,You get a small exp bar for it. It would increase by how much you use that cert's abilities, Which in turn would increase the effectiveness of the cert. To counter the ability to learn all the certs, there could be a forgetful option where if you don't use a cert for an extended amount of time the bar would go down. Or perhaps limiting the amount of learning you can do.
This would distinguish someone who has just purchased a cert from someone who's been using it for a while. I could see how this could be overpowering in a sense, maybe someone could mold it better.
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