For instructional purposes it would be very interesting to be able to simulate stacked quantum dots even in the simple effective mass model. Issues such as bonding-anti-bonding states and even band formation can be studied.
I believe some prototype screen shots exist in the prototype advanced-quantum dot lab, that is not published.

Ideally one should be able to select the buffer material and the material composition of the quantum dots.
Also the assuming we look at a vertical quantum dot stack it would be nice to be able to simulate multiple quantum dots and various sizes.