Perhaps goes a bit with customizing weapons, but perhaps allow different forms of weapons. Ex: EMP in the ESG mines, self destruct stickyfoam, who knows.
An idea someone had before, mounting of turrets directly onto structures.
Another place for major overhaul is in the command system itself. Unlike many other games OP2 doesn't have very sophisticated combat unit controls. For example, you can't easily tell it to just 'follow' a unit, you have to use attack which might not be what you want. Grouping is kinda clumsy, you can use the number hotkeys to assign vehicle groups but IMHO it should be more like the original AoE grouping worked: you select a bunch of units and push "group." Then, when you click one of the units in this group, all of the grouped units are selected.
Adding onto selections, there should be a way to deselect units or types of units (rather than just saying '30 units selected', give the player a list and let them deselect a certain type).
Another 'useful' feature might be something like rally points from a factory. Multiple unit queuing might be a nice feature but it can be overused (perhaps allow it turned on/off as an option, off by default).