Someone commented that it was difficult to drill button holes without a drill press - it's easy to get them crooked or off-centre. So what about having an easily 3D printable drilling jig to keep the drill bit square and true?
Something like this:

Simple box shape that seats positively against the front of the case. A couple of pins fit in the A/B holes and the D Pad cutout so it would line up perfectly (in theory... this is just a quick mock up) and a couple of tubes let you drill the holes in exactly the right spot without the need for a drill press.