Custom Arduino with ATmega2560

nownuri:
Could you please confirm if the followings features can be achieved?

  1. programmable with Arduino IDE
  2. 3.3V compatible
  3. 16Mhz

It can.

Just run the Atmega2560 at 5V (so it runs within specification at 16Mhz) and use logic level converters on all pins that need to be '3.3V compatible'.