I've found that with USB TTL serial 'cable adapters' so cheap on E-bay it just doesn't make sense to mount a on-board FTDI chip. Just mount a female header to accept the adapter and with the money saved I can buy a spare ATmega1284P chip!
"male" header?
By leaving out the FTDI chip, you also get a board that draws less quiescent power, and can
be used in low-power apps more easy. Plus you don't need all the parts in the power switchover
cktry between USB and power jack.