In addition to metal costs to late game magical items, one could always consider metal as a cost for city improvements. As an example, the Guardian Idol has a 10 Crystal cost associated with it. Surely there are improvements scattered around the tech tree (especially in the mid-late game) that requires metal for there construction.
As low hanging fruit, the improvements that improve metal collection should have an initial metal investment:
Smelter => 2 metal to construct
Foundry => 5 metal to construct
Large Foundry (parrotmath's wondersbase mod) => 10 metal to construct
Ironworks => 20 metal to construct
Even with that, it's peanuts off your endgame metal supply....maybe accounting for 50 metal...tops.
So, other structures that could use metal cost:
Lumber Yard => 2 metal to construct (saws take metal)
Timber Mill => 5 metal to constuct (saws take metal)
Warrior Temple => 5 metal
Weaponsmith => 5 metal
All the weapons from the techs Enchantment, Magical Forging, and Arcane Weapons could have metal cost. Doesn't have to be as high as their non-magical counterparts, but I think magic should be harder to construct as it generally is better.
Arcane Armor should also have a few more armor types available. Why only the one? Why not Arcane Plate? Why not Arcane Chainmail? Can't there by an Arcane Cloth armor? Naturally metal should be considered for these as well (well, not the cloth).
With all of this in place, one could conceivably spend 200-300 additional metal throughout the coarse of the game, and perhaps in conjunction with reducing the rarity of Iron Ore and Crystal Crag down to 250 and 250 respectively, it will be enough to make Iron Ore a valued resource again.
I'm going to see what happens with the 1.2 patch, but I'll seriously consider putting together my own mod if it's not addressed...