I think you are overcomplicating your design. Although an ATmega32U4 (as used on the Arduino Leonardo) has a significantly higher current consumption than an ATmega328P, you can still expect to run it in power down sleep mode, with WDT enabled as a possible wakeup event source, for over a year from a single CR2032 coin cell.
Program it to be a USB mass storage SD card reader when USB is connected and to run your data logger code when USB isn't connected, and put the money saved from chips to support a dual master SD card interface, dedicated USB SD card reader and USB hub or switch into a better higher capacity battery and you should come out ahead on operating battery life