Actually it kinda depends on how you play the game. A lot of the equipment you can put on your units cost more amounts of Material, Metal, and Crystal. I find early game I do have a lot of extra Materials, Metal, and Crystal but once I unlock armor and magic items I burn through my reserves really quickly becuase gold is also the most common resource. So I end up with gold left over and not much of the other stuff.
However if I focus mainly on my champions or poorly armored units I have large reserves of resources left over that continue to stockpile. Since most of those items are heavy on gold cost and light on anything else I tend to run into the same problem as you. It really depends on what your building as to where you resource go.
I do think there should be more options though as Metal and Crystal are only used to make troops. Several buildings at least use materials and so does the majority of early units.
The other source of issue is that since gold is used for upkeep your income for gold is constantly decreasing as your empire's army grows. Which is why late game I tend to focus more and buffing up my units with armor and burning some of that extra materials.
