I agree with having an alternative to random generation from the markets for some of the rarer items, like having guild quests that open up options to purchase the specific items directly from the guilds. That is already possible with the Fighters', Servants', & Mages' guilds through their shops for Dragon Bones, Writs of Exemptions, Oblivion Potions, and Unstable Concoctions. I already save-hacked to add Dragon Leather to the Workers' Guild, Elegant Chokers & Hand Cuffs to the Servants' Guild, and Energy Crystals & Gems of Energy to the Mages' Guild. This would also make the accumulation of Guild Points passed the mid-point of the game (after all the upgrades are unlocked) still worthwhile. Doing mini quests to, let's say, find and bring a renown herbalist to the Mages' Guild to add Blue Moss/Salvia to that guild's store, or acquiring an Arachne slave for the Servants' Guild who adds Ethereal/Magic cloth to the Servants' shop. It doesn't even have to be people, maybe so much as a mix of coins and materials plus a time delay to upgrade the Workers' Guild with an arcane forge that puts Adamantine into their shop, or the clearing of each type of hard dungeon makes the Warriors' shop carry a limited quantity of Crystalized Ether, Fire Rubies, Earth Shards, Eternal Ice, Chitin, and Ogres' Teeth as NPC guild explorers pawn off their finds from the recently cleared locations.
Story-wise, the protagonist is tied rather extensively to the guilds so it would make sense that the guilds are still important go-to locations for un-farmable resources.