I also back up drobear ssh keys /etc/dropbear/dropbear_*_key and bluetooth pairing information in /var/lib/bluetooth.

Best is of course to boot from mmc. Then when you upgrade internal flash to newer FW you simply mount old rootfs on mmc card and (gradually) copy all things you would otherwise forgot to backup (and there is always something forgotten in older system :-). Most times you can even boot older system as is and run the graphical backup tool later but of course you cannot count on that.