The metal/crystal split is to allow for some ships and structures contend for resources separately from each other. Like force-fields, riot-control starships, plasma seige starships, and missile frigates all contend for resources pretty strongly with each other, but not very strongly with most turrets, bombers, bomber starships, and fleet starships, and vice versa. This gives an interesting dynamic between choosing bonus ship types, starship types, and what planets to take.
As Diazo mentioned though, the recent harvester and manufactory (the converters) buffs may have made this dynamic much less of a factor, especially mid game and beyond.