Hi Radu,
Reading through the other posts regarding firmware updates. Perhaps if you added an SPI or I2C (depending on what IO is left and available on the ATMega) SRAM chip you could use the new json api to push a hex file into the sram verify it then hand off to the bootloader to read the SRAM and flash it.
You could also use the SRAM for temp storage when not being used to buffer firmware images.
Only downside is adding a couple of dollars to the BoM in the SRAM and passives.