It's critical that [materials, repair, buffs, and potion] services remain in the players' hands otherwise the game developers turn back into a central planning entity where they attempt to keep prices above some market rate, or worse, set the market rate.
Regardless of whether the game directly provides these services or not, the game indirectly influences the difficulty of creation which is nearly the same thing. In the case of materials you'll probably want some kind of difficulty adjustment process with stable issuance to maintain scarcity. With things like repair and skills, I guess those could be arbitrarily set.
My favorite form of monetization in these environments is tx fees (or a sales tax) - it's simple and transparent. My second favorite is paying for aesthetic and feature upgrades (like your paid guilds).
Player-provided services, like repairs, upgrades and item creation, would be based on the level of the job. Where I see the game devs having control is the "drop rate" of raw materials in the form of how many monsters spawn in an area, how fast they respawn, and the same with materials dug out of the ground. That could be adjusted based on server size similar to a difficulty adjustment.
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