If you're using a PC, you'll get more "power" through the 5.5" pad. The smaller pads can do more work on the PC where the opposite is true on the rotary.
I think it is a no brainer for PC users. The 5.5" pads are much cheaper and actually allow the PC to do the job. Might possibly cut down the amount of passes one may have to take or overall work time on sections.