I'm a little surprised that the shop doesn't have an 'exchange' where the merchant is willing to change whatever resource you have into another at some 'fair' ratio (fair for the merchatn......not for you).
This way, if you needed metal, but didn't have it, you could convert crystal for your purchase....but maybe at a 3:1 ratio or something like that.
That idea has been up before, but it will remove trading with the other factions.
What makes trading with the other factions interesting is that if you give some faction 1 trillion iron because you need crystals, you will see him start fielding fully armoured units. (So there is repercussions to you trading randomly). IMO this makes an exciting flow for trading.
Not saying its perfect for everyone, but still interesting 
Iron will never leave until used, same with crystal, if you trade it to other items someone else will hold the iron now, to use it.
Sincerely
~ Kongdej