There is a reason: the Flash memory on the device, 1Mb in total, is divided into 128kb sectors. We currently use the last four sectors to store one user preset per sector, regardless of size.
What would be much nicer is to have minimalist filesystem to store presets and other resources, e.g. samples. Then any number of user patches (most are < 64kb) and other stuff could be stored as long as the total size is not exceeded.
Problem is that with flash memory you can only delete entire sectors, so removing or replacing a patch becomes a little bit complicated.
I've been working on this functionality since some time... There's a dev branch in OwlWare, and it is also part of the new OpenWare firmware.
OpenWare is planned as the next gen firmware for OWL and some new devices we're working on. I've not got any exciting news regarding OpenWare at the moment, the code isn't very mature and doesn't yet work with the OWL codec. But we're actively developing it, and it is a key part of the roadmap!