I had considered that. Although, some projects have had very compact enclosures which makes access to the SD card not easily accessible.
My current prototyping endeavor is to add a 328p as an ISP and let that do the programming of the Arduino then write to the SD card. My thought was also that if I had the SD card already there for storing the active source, then it could also be used for data logging. Of course if I have to consider large SRAM usage, I may have to revisit the idea entirely.