I think the weapons are going to be unique to the story line and so this would make our weapons r/ex like in secret of Mana.
So Roy started with a rusty sword killed some rabites till it was a dusty sword and got some static ability and WS out of it. Back at the town Roy picks up the new mission GL rank 1 test for Gladiator. Roy and friends are whisked away and leveled capped to some town having earth quakes. Roy and friends fall down some hole where some big boss mob is there. After the boss was killed the towns folk gave Roy a sword ore. Roy gets back to main town and uses his Smith to upgrade his sword to rank 2.
I think the whole where down of the Equipment is just until the ability's are gained from them. After that its just a simple repair and resell if its not r/ex.
Roy's mage seemed to be capped out in skills so that's why he didn't take his staff to a wood shop.
I think ability's from the weapon are free and don't need ff9 bubbles. But if you change weapon to something else you would need to add the bubbles in to get the ability back.
EX: use wand to learn cure. while wand is equipped cure wont need any bubbles to use. but switch over to sword and now to get cure back you would need to set the bubbles to use it.
I think this is going to be a very heavy CS mission/quest driven game sort of like what SWTOR is looking like.