This is more an eye candy suggestion than anything else.
I think it would work very well to remove the right hand menu from the base view.
Then, when the user clicks on a building, like the research facility, they see the research window, or when they click on the hangar, they get the equip aircraft screen.
To build a new building, click on an empty space, which brings up a list of building types, which you can select and put in place.
The base inventory and buy/sell screen can be accessed by clicking on the stores, etc.
I would prefer this system than the current one, it would feel more intuitive.
Would it be hard to implement, or would it be relatively straightforward to rearrange the gui?