Since many keys are listed in "ingredients", there could be a recipe to craft lockpicks (i would appreciate that).
It would be fine in my opionion if there would be chests and doors that can only be opened by using the right key, and locations you can't reach with teleport or jump. See, i don't have a problem with bypassing stuff or doing it in a different way, but there has to be some disadvantage to it, or something that equals things out (so if one spends 20mins to solve the puzzle and get the key, and someone else just bruteforces the door/chest, something should punish him for doing so). i am fine with the equipment damage, but damaged loot would also be okay (other games did this). i don't have a problem with different ways to use chests, also "unlock"-spells are fine, but just bashing stuff open with no disadvantage seems wrong.
with chests, what i would like to see is, that using spells or weapon dmg to open it damages the items (so that you can repair them), or has a chance to completely destroy them (so that you get only some leather or cloth scraps instead of armor or robes).
doors, i would say there should just be doors with that high levels that it would take hours to bash them open. most doors are level 10 in cyseal, takes long too, but is still sometimes the easier way to do it.