Personally I like Soul Gems, and also believe they should return. But again, there should be a couple tweaks from Oblivion in my opinion:
1) Don't Make Us Invincible - Invariably someone finds a flaw in the crafting system and either makes themselves indestructible/invincible (e.g. 100% chameleon) or uses the system to create godlike weapons (e.g. Soul-Trapped, 100% Magic Weakness, 35 Fire Damage, 100% Fire Weakness Swords). The core game engine simply shouldn't allow players to do things like this. Mods and console commands exist for that when people want to use them.
2) Randomization - Crafting an item with a certain set of materials doesn't necessarily have to always produce the exact same item every time. If I take a hootchnagger, a polywhiffle, and an emerald banana to the crafting enginge, who's to say that I should always end up with Whatchahoozit +15 Fire Damage? Why not make it a small range of possibilities when doing the craft, perhaps even with a very small chance to make an exceptional or "perfect" combine that has stats well beyond the standard range available when using those components? I think that could add some fun and an element of suspense when doing crafting that is somewhat lacking in previous systems.
1st, I really would like to get my hands on a Whatchahoozit +15 fire damage. That would be cool.
2nd, and more serious, I don't know if I really would like randomization as I think most players would like to know exactly what they are getting when they enchant, not just at master level. Also, this could lead to saving before enchant, enchant, don't get the "perfect" or "exceptional" result, reload, repeat because they feel like they are being cheated if they don't. Now, of course, you will say that's up to the player, but I really think we should know what we will get if we spend the time to enchant. I would like more control and more options though. And not the OB default, weapon gets on strike, clothes/armor get constant effect. I prefered MW's system that way.