Atmega32U4 can be reprogrammed for other functions, instead of USB only. Atmega2560 by itself has no USB interface.
FTDI cannot be reprogrammed, and are pricey, $4.50 USD per chip in small quantities. Price hasn't changed in the 9+ years I have been active in Arduino. No crystal is needed.
Atmega32U4, $4.20/chip in small quantities. Adds up when buying thousands, millions. Crystal is needed.
Could argue the two chips are probably similar cost when buying for worldwide production. But the FTDI loses out on programmability. Then again, how many folks take advantage of that?
On the other hand, the Atmega32U4 seems easier to damage when there is any power fluctuation, while the FTDI seems sturdier in that respect.