For the part about the weak enemies, I think allowing the player some settings with regard to weaker foes should be added. For example, there should be an "Intimidating" stance that causes weak enemies to run away and you don't have to bother with them. However, you might want to kill them for some easy EXP or money so there should also be a "Friendly" stance that has them attack you like normal.
As for a loot priority system, that sounds great!