Changing the keyboard layout would introduce a lot of significant compatibility problems. Remember, most software on the C64 scans the keyboard directly, and so if you change the layout, it will just break things.
In terms of learning typing, I don't think this is really a big deal. The letters and numbers are where they should be, and yes, the Commodore-style layout is a bit weird, but the C65 is not as bad as the C128 on this front, in my view. Cursor keys are, for example, sensible on the C65. I find the variation between laptop keyboards to be at least as significant as the differences on the C65 to US or UK keyboard layout. And don't get me started on the differences with German and French keyboards (both of which I use on a regular basis). Compared with those, the C65 layout is still rather sane. Also, just like with SMS that had the most horrible interface on feature phones, people learn surprisingly quickly to work with what they have.
But, as with everything on the M65, it is open-source. If someone wants to make a French layout or whatever other layout version, they will be free to do so, but we will be sticking with a C65-faithful version in the first instance.
Now, for USB keyboards, this is only possible on the Nexys series FPGA boards. The final PCB does not (at this stage) have a USB port for keyboards or mouses. USB mouses can be used with an Amiga/USB mouse adapter, as the M65 provides transparent 1351 emulation when you plug in an Amiga mouse. This is partly keeping with our goal that the M65 has only 8-bit processors, so no hidden USB stack will be there to harbour a 32-bit processor. Also, we ran out of space on the back for connectors.
Paul.