I don't know about embedded Linux, but as for the drive, you could always swap the flash drive for a larger one; or maybe get a PCCARD one, if there is a PCCARD slot. In my opinion, with as little as 6 GB you could get along quite comfortably, repositories and all, while every GB over that would further increase the usability. You could also include a removable USB thumbdrive for data. Or you could concentrate on using it prevalently as a thin client, if you have access to a wireless router and a capable desktop to hold the bulk of your data.
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