The Iridium Stores can be upgraded to better improvements (specifically to a 15% income, 15% influence, +2 levels to adjacent wealth/influence structures improvement and then to a +25% income, +25% influence, +3 levels to adjacent wealth/influence structures improvement) while the free markets cannot, at least from what I see. More expensive to maintain, more expensive to build and upgrade, yes, but probably better given sufficient time.
