Here's my idea.
-You can only enchant suits or sets. So you can have full iron body, and maybe Steel boots. So now the only way to gain the benefit of the enchantments is to wear the set of the iron armor and the steel boots. You cannot wear any other enchanted items unless you disenchant the items and remake the set. (You make your own set out of anything, it doesn't have to be the same material.)
-Each item equipped on your character has an enchantment level, and the magnitude of the enchantment on your outfit is determined by it's average.
-Disenchanting the set destroys the souls and sets the armor condition to 0
-The enchanting skill comes into play by giving you more spells to choose from. Spells you own shouldn't be spells you can put on armor, there should be enchantment exclusive spells. Also, higher enchanting skill will increase the enchantment values of all items to a degree proportionate to the level of the skill.
-Weapons should remain relatively similar to Oblivion, where it has charges and stuff, but a perk for Enchanting should be recharge over time.
So as you can see, I feel if Morrowind level of customization were to return, there are ways that it could be balanced.