I would suggest in comparison of the size of the building (small,medium,big, ?gigantic?) that you have more than 9 departments each building. You can f.e. only sell 4 products each shop, that´s unrealistic for me, in comparison of the area (and ground prices the building costs).
So my idea is:
In comparison of the size of the building (and area needed), you have space for
4 departments for very small buildings (2x2) 9 departments (like it is yet) for small buildings(3x3), 16 departments for medium buildings (4x4), and 25 departments for big buildings (5x5), 36 (6x6) for huge buildings, 49 (7x7) for gigantic buildings.
In the other suggestion there was my idea of more than one floor and upgrade it.
In equalization the cost of the bigger biuldings will raise and the monthly costs which each available department.
So a here called "very small" building with 4 departments also can only upgraded 2 times, (or build up currently with 3 floors (including ground floor) in order to get not too high, in order to avoid an unrealistic small "Aunt Emma" skyscraper.
Buildings with more ground area and size than later you can upgrade higher.
As a gimmick my another idea would be you choose the floors you have. so you can have a ?small? ?supermarket? with a space 1x1 with ground-, 1st- and 2nd floor or a ?small? ?supermarket? with groundfloor, 1st basemant and second basement (cellar).