I looked on Mouser for an ISA slot connector. I found a whole backplane ?? for $28+. I looked other places. Briefly. I found nothing.
Looking on Mouser for a PCIexpress connector, however immediately gave me this:
PCI Express / PCI Connectors 98P CARD EDGE ASSM VERTICAL
A 98 place socket for $0.78 quantity 1, $53.40 for 100. A common, inexpensive part. Nice.
I suggest that the PCIexpress (x8) connector would be more appropriate for Commander X16, just based on availability. 98 pins may seem like a lot for an 8/16 data bus, but:
The 65C816 has a 24 bit address space.
For EMC and signal integrity reasons, every signal should have a return path (ground). Adding a dedicated return for every signal will make the bus much quieter.
If we were to expose all 38 signal pins from the 65C816, plus the extra de-multiplexed 8 address bits, and then give every signal a ground, that leaves just four pins for Vcc. That doesn't seem all that extravagant to me. I'm not saying we should directly expose the full CPU bus, but having room to choose what we want to share is A Good Thing(tm).
Any (weak) argument that this would tempt people to insert PCI express cards would also apply to ISA connectors. You can just reverse the socket or change the distance from the edge of the motherboard so a normal PCIe card would not even fit.
I'm not suggesting that we support PCIexpress, just that we use the same mechanical connector because it is cheap and readily available.