Ability to block some storage to allow for "free space" and not have to have the whole container fill.
Inventory management, more precise controls, i.e. shift clicking to move stacks is flimsy.
The availability of a toolbar AND a building bar for shortcuts.
Separate slots for Blade Runners and JetPack. Why can't I have both at the same time?
Central location for management, perhaps a computer mainframe structure that can control all items that are linked via power poles.This way you can set names to buildings, set their recipe, check their status, check power usage for that section of the grid etc.