Alright more ideas...
Special unique/story characters that you can find while exploring with unique skills, these will stay in your team permanently, but will ask a fee every times they are released on a mission, like mercs, but in the permanent roster, though unlike mercs, their fee is fixed, they don't cost more as they level up. (I know you had plans for special characters already, this is just another way to get some), they could also have their own story line and quests as optional quests.
Powerful consumables that once used, are lost, they are more efficient than the reusable consumables.
Purchasing unlockable hairstyles, i want a fancy ponytail for my wildcat conqueress :p (I am very biased, i just love wildcat, so deadly)
Purchasing unlockable cosmetic clothes that can override the functional armor.
An influence system that allow you to raise affinity with your team mates, purchase them gifts. Affinity could do various things.
Tax collector zombies! (jk)
I'll post more if i brainstorm again!