I have to say, it's not easy thinking of things to improve CircuitPython. Adafruit and the CP support community have been doing a great job supporting and moving the platform forward. Thanks!
I think adding intuitive flash file system commands (ls, cp, del, etc..) to the REPL would be a nice usability improvement. I know you can import the OS library and use the library functions to manipulate the file system, but the output and the interface isn't really optimized for an interactive experience.
*edit* As I think about the above suggestion, I'm realizing that I'm probably an usual use case as the first thing I usually do is switch the storage.remount mode so the microprocessor has read/write access rather than the host computer. It's only in this mode that the file system commands make any sense.....
I would also love to see some way of dealing with sensitive data on the flash. The secrets.py file could obviously benefit from better security and applications like password vaults that utilize HID keyboard input are another potential beneficiary. I know you can disable the usb_drive and REPL in the boot.py file but unless I'm mistaken, that means you would need to completely erase and re-flash a device every time you wanted to make a code or data change.