And how about this?
The Skill books/tomes the Sage is able to research are specifically for Attack, Defense, Support, HP, or Auxiliary Champions. And you can't choose what he or she manages to research. It's random. That way the tomes the Sage researches won't decrease the value of the tomes that can be used for any Champion.
EDIT: Additionally, if there was a Smith Auxiliary Champion, the weapons and armor he could craft would randomly be of a specific Affinity (depending on how the materials combined while he or she was forging the item), so only Champions of a certain Affinity could use them.
I also kind of like the idea or possibility of there being cursed weapons and armor in the game. Gear that would randomly debuff your Champion or during a battle or have a specific debuff or debuffs that it always applied. Depending on the type and severity of curse. And you would need an Enchanter or Sage Auxiliary to either identify gear before your Champion equipped it or take it off after your Champion equipped it. Though you could pay more at the (possible) Tinker Shop to remove it as well. However, it would cost twice as much.
EDIT #2: Actually, some Artifacts might be cursed magically (and so the Enchanter or Sage could identify and help remove them), but other Artifacts might be cursed by a god, demon, or other supernatural being or entity. In that the case of the latter, a priest type-Champion would be required to remove the curse and safely un-equip the Artifact. Most players would already have or could easily obtain such a Champion. However, some curses might be so strong that they must be taken to the Temple (new possible location in the Bastion) where a high priest can remove the curse on the item. While the Temple wouldn't charge more for removing the Artifact, a small donation of 0.5 x the normal cost of removing an Artifact would be suggested (i.e. necessary).
Oh, the levels of the curse would be equal to the rarity and rank of the Artifact.
Uncommon Enchanters and priestly Champions could remove Uncommon curses up to rank 3.
Rare Enchanters, Sages, and priestly Champions could remove Uncommon curses up to rank 6 and Rare curses up to rank 3.
Epic Enchanters, Sages, and priestly Champions could remove Uncommon & Rare curses up to rank 6 and Epic curses up to rank 3.
Legendary Enchanters, Sages, and priestly Champions could remove Uncommon, Rare, and Epic curses up to rank 6 and Legendary curses up to rank 3.
Legendary curses of rank 4-6 would require a visit to the Temple in order to remove them.
Perhaps an Enchanter could also slightly lower the cost of upgrading Artifacts. Uncommon Enchanters by .10% / Rare by .25% / Epic by .5% / Legendary by .75%. Having additional enchanters would further reduce the cost up to a limit of 5 times. So, if you had 5 Legendary Enchanters in your ranks, the price of upgrading Artifacts would be reduced by 3.75%.
EDIT #3: Cursed Artifacts could also be purified at the Temples, removing the debuffs and making them safe to use. However, this would cost 3x the amount needed to remove the Artifact.