Nice idea innociv!!. I got some more idea to share too. How about there's 1 upgrade blacksmith that do as you explain, upgrades things. But i think starting with basic gear that has no stat boost at all and start upgrading from zero is better, no need to buy any base item at all. This way it'll become like a skill tree with gold instead of exp. But it will reduce the complexity to choose between every base items and have to consider all upgrade paths and stats.
Now for additional idea, how about we have 1 more shop, to add 1 "special passive ability" to items. Like you choose a boot, and add life stealing on it or choose a helm and add reduce cooldown. Just add those "Passive" things on it, to reduce complexity of the stat upgrade tree.
And for another ultimate shop, add 1 "active skill" to your items. This way we can throw away the Artifact shop and just put this shop instead. Less items with the same result. Of course this active skill upgrade should cost more gold to do than PASSIVE and normal stat upgrade.
This way people will have it easier to get what they want. Let's have a look at the example :
1. i need some thing that boost my armor!! ---> go to stat upgrade shop to get upgrades in armor branch.
2. Damn i can't run away from my enemies, i need teleport!! ---- > go to Active skill upgrade shop and get blink upgrade on one of the item
3. our team lacking in overall damage, what should i do?? ----> go to Passive skill upgrade and get +Damage Aura upgrade.
And for the dev team, it's easier this way since we no need of new items and unique skill tree upgrade for each items, just 5 trees for stats (1 for each type helm, boot, armor etc.) 5 sets of passive skills to upgrade (1 for each type same as for stats) and 5 more sets for active skills.
Why having different sets for each type of item? That's for balancing purpose. Say, you can't make all your items have +25% walking speed, or you can't have all Active chain lightning for 5 of your slots to spam (making it have the share the same cooldown just make it frustrating for new player that think they can make uber chain lightning spam).
Hope these idea help out 