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With the introduction of company leves that use up a leve allowance and award seals I think they should do similar with guild marks. Have guilds issue their own leves that reward only in guild marks and use up a leve allowance per leve. If players want mostly exp and gil then that's what the adventurer's guild is for.
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Someone already suggested a reasonable option, being able to trade marks for gil. Not that I have an issue with the system anyway. I have all the guild marks I need plus like 70k spare but I'll be happy when new abilities comes out and I already have more than enough. xD