I finally had some time to assemble a second unit of the version 6 prototype, this time with the 6x6x6mm switches, and the "springy" caps that have a cut through the hole. It works surprisingly well:

I still need to resolve a few issues: the buttons are too high, making the caps stick too high from the case, the fire buttons rotate and get stuck, and generally look bad, and the D-pad has some sharp corners which are a bit inconvenient.

So I have another set of caps on order from Sculpteo (that was an experiment, but it turns to be very expensive):

Those have less lee-way around the edges and smaller holes for the shorter switches. I'm also testing a different way of making those springy cuts in them — we will see how that works. Hopefully being lower and having less leeway will prevent rotation of the caps.

I also started working on a final version of the laser-cut design, with all the parts on one 100x100x2.5mm sheet of acrylic, for easy cutting. The middle layer of the case had to be split in half for that. Here I used round fire buttons, so the rotation shouldn't be a problem.