Something I would like to see is a good way to connect to the GPIO pins on the Raspberry Pi externally for additional functions. I am trying to figure out a clean way to add an XBee to my OSPI. The best way I have thought of is having the Raspberry external to the enclosure. I have breadboarded a daughter board that stacks on the Raspberry, which is external. The connector is a stacking type so the OSPi could connect onto to it that way. Not as clean as I would like.
Also, have cut outs on the top enclosure so USB devices can plug in as well as hard connected Ethernet.
For connecting to GPIO pins, you can probably use jumper wires similar to the 8-pin and 3-pin cables. But if you have a board designed to sit on top of RPi, then you have to either keep the RPi out of the enclosure, or just remove the top cover.
I will consider adding cutouts for the Ethernet and USB.