On the subject of crafting in general... I do believe merchants should be able to do commission work for you, and vice versa. Commission work for goods you want should probably be the most powerful but also the most expensive.
I don't know about the commissioned items being more powerful right off the bat, unless you just meant that you could commission a Daedric Mace at level one if you had thousands of gold. But I think the true power of commissioning items is having them improved for you. But that's a whole other can of worms that I need to think about.
@carrotfeets
I've been studying how Smithing has worked for a while before I started my work, and I think a lot of the things you have said are addressed in what I wrote. Perks give a few static bonuses across all smithed gear, and in order to improve gear you need the proper perk to do so in my proposed system. Learning how to make new gear is now covered by quests available at certain smithing levels. The only thing it didn't address is that there aren't unique items to be smithed, but I rather like what Darkside Eric said on the matter:
At the very least, that Perk aside, I would have liked to have seen the ability to make multiple types of each items. Like instead of just "Elven Sword" I would have liked to see "Elven Sword Design 1, Design 2, etc" as well as things like "Elven Short Sword, Elven Scimitar, Elven Sabre, etc."
I think it would have been nice to have more variations on items, especially if it affects item weight, damage, and attack speed.
Another example, I would have loved to have bucklers, kite shields, and tower shields of each tier. The type would be directly proportionate to item weight, armor, and movements speed reduction; with bucklers being light/fast/weak and tower shield being heavy/slow/strong. Kite shields would be the middle ground. That would encourage players to carry something depending on what they thing they will face. A person fighting a dragon would want at least a kite shield, while a person fighting a bandit with a sword would want something they can move with. And a Tower shield with the Deflect Arrows perk would have no trouble with archers.