Part of the issue with USB are that you need a CPU side USB stack/driver to control the peripherals that you plug into it and that it actually takes a bit of processing power to do run that. There are already USB stacks for the Amiga though so it must be workable.
For building a "power minimig" or "MiniMigV2" etc the 68060 makes more sense from a simplicity point of view. This is because the 060 is a 3.3v part whilst the 020, 030 and 040s are all 5v parts. The rest of the MiniMig (FPGA, RAM et al) is all 3.3v so attaching them will require voltage level shifting and different power planes for the two voltage regions on the board which makes it all more complicated and a lengthier process to build.
Of course the 68060 is harder to get hold of and more expensive...
Andy