I would like to suggest that weapon based magic combat be introduced into the game, specifically in the form of a staff. It could be made with two sticks, and another block on top (Diamond tip would be better than iron, gold, and so on.) The top of the staff should be an entire block of resource, so it's not too easy to get. Like a block of diamond, block of emerald, block of gold, block of iron.
Perhaps this staff could have a new enchantment table with different types of spells and some of the older enchants. Maybe every time you used a spell, it would take some of your exp levels as a way to power your new weapon, and keep yourself continuing the game. This would open the path for a new enchantment that would allow the staff to take less exp from you per cast, let's call this enchantment "Wizardry." Wizardry would come in different levels like unbreaking, sweeping edge, sharpness, power, etc.
This examples are NOT limitations. I'm not saying only a diamond staff would be able to shoot fireballs, golden have shock, and iron have frost (I will recap and add all of my spell ideas below). I would like all staves to have the option, so the player can decide what type of magic they would like to use.
Perhaps some types of magic would be resisted by mobs due to their biomes. For example, Nether mobs would be resistant to fire damage, mobs in ice/snow biomes would be resistant to frost damage.
This staff would allow you to shoot a magic ability of your enchantment choosing, while still utilizing much of the already existing features. Of course the top block would determine durability, the power of enchantments, and such like it does in the game now. With the magic resistance feature, the player would still need to take the time to make a staff of every type to be the most efficient in the game.
NEW IDEA RECAP:
Enchantment: Wizardry (multiple levels)
Spell Enchantments: Fireball (fire based), Shock (electricity based), Ice Shard (frost based), Hurricane (air based), Mud Slide (earth based, think launching a rock at someone), Tidal Wave (water based), Shadow Crash* (shadow spell, *requires an item from The End to cast every time, but does massive amounts of damage), Volcanic Eruption* (Needs an item from the Nether to be cast, but does massive amounts of damage).
I didn't see this post until after I suggested something similar, and I think there's a lot of different kinds that could be added. I think the devs would stick mostly to abilities already made by potions, but some interesting ones could easily be implemented.
Like a redstone wand/staff that can be used to activate redstone components from a distance, or one using bones and rotting flesh to make undead passive or even follow you.