Iron weapons Vs Crystal weapons

Typically iron is used to make "normal" weapons and armor. Crystal is need to make the magical/enchanted armor and weapons in the Magic Tech Tree. Typically Crystal is more valuable. Have you tried using diplomacy and maybe trading with a friendly neighbor some of your crystal for their iron? Otherwise if you know where some ore is, send out a pioneer and build and outpost. Then look towards the tech that will let you upgrade your mines so you will get more iron per turn.

I create a unit of each weapon type that uses zero crystal but maximizes all other aspects. There are trinkets that require zero crystal (ie. First aid kit, etc.)   I give these units the prefix "Town" or Tower" in front of their name (ie. Town archer") . The melee units come in the mounted/ non mounted variety. (ie. "mounted tower sword" or just "Town Sword"). Unmounted units sit in towns. Mounted units sit in towers or unique resources (ie. resources that give unrest reduction/research boost). These are the units I typically fight other factions with. They make the bulk of my general army.

 Of course my sovereign and top 2-3 heroes run with crystal laden troops using the prefix "King's"  (ie. Mounted King's Axe" or "Mounted King's Archer"). They also run with a Henchman specializing in healing if the hero cannot do the healing himself. These are the monster killers. They roam at will, solving quests  and killing dragons with little worry or regard toward rushing home to defend the capital.  The general "metal" army takes care of the wars. The one exception is that mages require crystal and are necessary for the wars, but I keep the crystal to a minimum. Typically used in just the staffs.

I do this because there is simply not enough crystal to wield a huge elite army.

So crystal weapons are just outright better then iron weapons?

In the power level sense....yes. Many also do elemental type damage which is better against many creature types....though there are those that are resistant to cetain elemental damage types....so build your armies with care.

The problem, or I would argue...balance, to the puzze is that there is only about half the amount of crystal on the map compared to iron. Combine that with the fact that you harvest crystal at half the rates as well, you in effect have only one quarter the amount. You'll most often be short this valuable resource. (which is how it should be.)

Currently the game outputs an overabundance of metal in the game so three shouldn't be too much trouble to trade AI factions for it.

Several of us in the community...and I'm sure Stardock as well....is currently looking to scale back iron ore in some fashion....or make it more important in some way.

I'm confident there will be a patch one day that will address this concern. 

Which is the best weapon, the crystal version or the "iron" version, does depend to some extent on where you are in the research tree. For example, upgraded weapons (e.g. boar spear, damage 9) can be better than the first level of crystal weapons (ice spear, damage 7). Magic weapons will do some magic damage though, which is significant if you're facing high armour troops. Staff wielding troops can devastate armies which would be barely touched by archers.

I usually give my troops the standard, "iron" versions of weapons, not least because otherwise you run out of crystal very quickly. The main advantage of crystal for me is actually in the accessories. Troops with standard weapons but good cloaks, amulets, rings, are much more powerful than without. Be sure to design and train units to take maximum advantage of what technology and resources you have available to you at that point in your game.

I've never checked this myself, do crystal weapons cost the same labor as iron or is it more?

If you have 2 crystal mines you should be OK without iron for at least 100 turns. Lightning hammers and staves go a long way.