weiterer Unterschied ist:
der R3 hat einen ATmega16U2 als USB Schnittstelle, R1 und R2 hatten einen ATmega8U2
das und weiteres steht aber alles hier http://arduino.cc/en/Main/ArduinoBoardMega2560
The Mega2560 differs from all preceding boards in that it does not use the FTDI USB-to-serial driver chip. Instead, it features the ATmega16U2 (ATmega8U2 in the revision 1 and revision 2 boards) programmed as a USB-to-serial converter.
Revision 2 of the Mega2560 board has a resistor pulling the 8U2 HWB line to ground, making it easier to put into DFU mode.
Revision 3 of the board has the following new features:1.0 pinout: added SDA and SCL pins that are near to the AREF pin and two other new pins placed near to the RESET pin, the IOREF that allow the shields to adapt to the voltage provided from the board. In future, shields will be compatible both with the board that use the AVR, which operate with 5V and with the Arduino Due that operate with 3.3V. The second one is a not connected pin, that is reserved for future purposes.
Stronger RESET circuit.
Atmega 16U2 replace the 8U2.