what I mean is, the linux port is r/o to the sdcard, instead of using the entire sdcard, have the user preferences and addition packages stored in a .img or.iso ( or something similar) therefore adding more ability to port/add programs and files to the os without a full recompile. this would also allow for better caching and (maybe) the use of a basic (but custom) pkg manager that points to a repo on github for addons, that then get put in a .img file to store extra data. Also, to answer your question, this is a poc (as far as I am concerned), but in the future, this may actually end up being a start for a full blown linux/desktop os on a 3ds, it may be slow, but imagine baing able to use github or wget, ssh, rdesktop... etc I am pretty sure they already have arm9 or 11 counterparts...
have you tried debian or ubuntu, If not you should make a bootable usb for lubuntu, you may like it...