There are two main differences between the new and old Arduino Megas. One, as you note, is the memory. The new ATmega2560 chip has 256kB. The old ATmega1280 chip had 128kB. That's the main difference.
But they also took the opportunity to replace the old FTDI to USB chip. That has always been a weakness with the Arduino design. They did an upgrade to an ATmega chip, which is somewhat better, but not as good as full USB. The Teensy, for example, has a great USB interface.
But none of the pins or other stuff like that has changed.