There is another consideration. If you use the same socket type to connect things that take different voltages (e.g. stepper motors, and 5V or 3.3V devices), it's guaranteed that some users will swap them by mistake and blow up the device, the Duet, or both.
Additionally, if you use USB cables to connect stepper motors, you would need to buy a USB cable (if you can find one with a high enough current rating), cut off one end, and splice it to the stepper motor cable - because nobody sells stepper motors with USB plugs attached.
We chose the connectors we used for a reason:
The Molex KK series connectors that we mostly use are widely available and easy to crimp (preferably with a suitable crimp tool) and the pins can easily be removed from the shells if rewiring is needed
The JST VH connectors that we now use for higher current connections are likewise easy to crimp and easy to disassemble. A PA21 crimping tool does both VH and KK connectors.
The RJ11 connectors that we use for CAN except where space is constrained were chosen because twisted pair RJ11 cables are very readily available in some countries, and not difficult to make up using readily available and inexpensive tools.
The other connectors that we use only where we have to are:
Molex Microfit 3.0 (which are favoured by E3D) are not difficult to crimp, but it's hard to remove the pins from the shells without an expensive tool. We use them only where we need a higher rated current than Molex KK but don't have the space (i.e. on the Smart Effector), or where we specifically intend to support E3D sensors.
JST PH (used on some other boards and on stepper motors) are harder to crimp than Molex KK. We use them on the Tool Board for the stepper motor, to save space.
We use JST ZH where space is tight. These are hard to crimp because they are so small, however connectors with pre-crimped wires are readily available.
We've moved away from terminal blocks because OEMs hate them, and they are only good at carrying high currents if the proper ferrules are crimped on to the wires. The barrier strips that we now use for power in and bed heater out on Duet Maestro and Duet 3 are more forgiving.
