Switch to microcontroller with integrated USB.

[damellis]

For example, the AT90USB1286-AU. That way, you wouldn't need an FTDI header and could use the Mini-USB connector (or a Micro-USB connector) for charging the battery and re-programming the microcontroller. This would save some space, I think, although the chip is slightly bigger than the ATmega1284. This is a fairly big change, though, so it probably won't happen for a while.