health and Injuries:
In addition to a general health bar, each body part has it's own health bar which when depleted that body part becomes vulnerable to injury(burns, broken bones, deep lacerations, nicked/severed arteries,etc). also there is a chance of dismemberment which(with exception of decapitation) you can survive if you have high enough skill in restoration/alchemy or you reach a healer before you die from blood loss, in the instance you lose a limb you can get a prostetic (which can vary from a none funtional wooden one to a macanical dwarven one).
skills:
the effectiveness of skills increase naturally without perks as they level up(perks still exist they just aren't manditory).
also there are different character animations based upon their skills, for example characters with high one/two handed skill make tighter more accurate swings, characters with high achery/marksman skill are capable making small more accurate movments when aiming in order to hit their target in the right spot(also they can see further), characters with high block find it easier to follow enemy attacks making it easier to to block, dodge or even deflect them. bringing back the hand to hand skill, in addition to the effectivness of you punches increasing, as your skill goes up you become physically tougher(your bones are harder to break).
magic:
when it comes to casting spells not only does the cost of the spells go down as your skill in that type magic increase but also the time and effort. for example if your character is a novice in destruction magic and they try throw a fire they would need to use both hands and do a series of movments(much like casting a master level spell in skyrim) inorder to create the fireball, but as there skill increases they will be able to create the fireball without doing all of those movements but they will still need to both hands and afew moments to charge up the spell, then they will be able to do it with one but still need to charge it up and finally they will be able to cast it instantly(or charge it up to make a more powerful version of the spell). also certain spells scale up in power (like telekinesis, at first you can only move small objects but eventually you will be able pick up and throw large objects and even enemies).
races:
each race should have abilities that make your experience with that race different from the others. each race should have several variations( like bretons have have high rock bretons and reachmen).
vampires and werewolves/creatures:
as you feed your abilities increase, like your attack power increase, you can run faster, jump higher and farther)
to be honest I thought of afew other things but i can't remember them at the moment.