While an Arduino128 or the SiameseDuino is an excellent option for new purchases, I think an IO expanding shield with a second I2C slaved Atmega128 on it and a second set of IO pins might be a good option for existing Arduino owners.
There are I2C data-expander IC chips already. They connect via I2C and give you as many virtual digitial I/O pins as you care to buy chips for.
While a 2 mcu arduino may have its uses, extra I/O is a silly reason.