My take on the first issue, is it wouldn't be a problem to have unique items, but balance still dictates that these can't be over-powered. Perhaps they can have certain attributes specific to that piece of equipment.
In this way, unique items can encourage a further specialisation later in the game (upgradeable unique weapon gives a damage bonus to undead, if you are a paladin who can use the weapon to its full potential. And as you upgrade it the weapon becomes more potent against more powerful enemies).
You would still have cause to keep and use equipment that you've been lovingly upgrading, for they by right should have the widest range of customisability/upgrades.
I don't like the idea of hard class restrictions either, so unique items would be able to be worn/wielded by any character, but only those with the proper training/class will get the special bonuses associated with it.
Personally as a hoarder, I also noticed a tendency to keep stuff 'just in case', and end up with a huge stockpile of materials, scrolls, gems etc.
To deal with this issue, unique crafting materials can only be used to craft specific, high level items, or when your own armor has reached a certain tier of quality. Materials shouldn't be too hard to obtain, and some games (like Kingdoms of Amalur) have even allowed players to 'break down' armour and salvage crafting materials (an exception can be made for unique items, which cannot be broken down and salvaged).
Again, if hard limits to upgrades isn't desirable, then have the NPC smiths advise you to save it for later, but will still upgrade your current equipment if you insist.
Adding this level of flexibility would mitigate the hoarding syndrome and make the upgrade curve smoother.
All this in addition to the suggestions Somna put forth, like gating upgrades by region/upgrade time/cost as and when its necessary.