Wood- used for bows, ships
Metal- used for metal weapons
Horses- used for mounted units
Materials- used for building construction
Crystals- used for high-lvl magic buildings, magical equipment formulae (sword +1 would require 10 metal, 10 crystals), sword+5 might require 250 crystals (it should be exponential)
Elementium- lategame material.
The old standbys:
Mana- used for spells. 1.1 magic system and all
Gold- used for many purposes
I don't think we need more then that.
From there, buildings (with prereqs) should be used to provide access to higher lvl stuff. Wood and Metal can be converted into materials, but not vice versa.
Iron weapons might require a blacksmith (and tech)
Steel weapons might require more tech, and a better blacksmith.
Elementium weapons would require Elementium, and a master blacksmith (which once elementium is discovered, each blacksmith would have a chance of becoming a master class blacksmith. Higher-lvl blacksmith buildings would provide a better chance. This would be a random, free upgrade, perhaps a hero unit that can be attached to a city?
Markets would allow resource trading between civs. Instead of trading treaties, sovereigns should with a market be able to put their excess resources "on the market" (think Sins perhaps). The game would determine the cost based on what sovereigns put out and demand for each player. Having access to more civs means access to more excess stuff and lower prices.
There does need to be a way to upgrade weapons. If you're in the proper town. It should be a replacement for building a new unit (can't build a new unit and upgrade at same time)- but would be faster (not cheaper), and the unit would keep its experience.