Have you considered maybe using the Inhaos Buono Mega 2560 (see a; b)?
As far as I can tell, it is pretty much identical hardware as the Arduino Mega 2560 -- including the ATmega2560 processor -- except it has a selector to run the ATmega2560 at 3.3 V, so its I/O pins can be directly connected to 3.3 V modules.