It's been done on other cards as a user-selectable option. CycloDS is an example. I have seen a separate SAV directory break some 3rd party utilities like Rominator 2008, which has an excellent SAV backup tool that looks for the SAV files in the same folder as the ROMs.
This option was mostly used as a crude SAV manager in the CycloDS. For example, you keep your SAV files with the ROMS then when a friend wants to play to change to Alternate SAV location and their SAV files are in the separate SAV folder.
Of course since AKAIO can already handle multiple SAV files, the above example is not a reason for this to be implemented in AKAIO.
IMHO, this feature isn't for the masses.
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