Well, if your going to replace the battery cover, you could replace the 2xAA batteries with a li-ion or polymer battery of 3.7V also, and then that would give you room to place a small circuit in the battery compartment too, and because of the 3.7V, you wouldn't need to step the voltage up, so the 2x wouldn't draw so much current in stepping that up, giving the end result of not needing quite so much battery capacity for the same life.
Or perhaps you could sandwich two batteries together in the same space as 2xAA, and use one of those to power the usb host or harddisk, and therefore only having a small bulk on the back of the device for the harddisk.
The possibilities are endless...