The MEGA 2560 is designed for more complex projects. With 54 digital I/O pins, 16 analog inputs and a larger space for your sketch it is the recommended board for 3D printers and robotics projects.
Starting with hardware, the Arduino Mega is based on the Atmega2560 microcontroller. In the iteration that is found on the Mega board, the microcontroller comes in a standard TQFP 100-pin package.