The prototype is clearly an ATmega32U4. The Atmel logo is clear, you can just about make out the part number, and it only has 44 pins.
While the Arduino did great things, I don't really see much point in continuing with 8-bit MCUs as hobbyist platforms. ST's Nucleo boards, for example, are far more powerful and very cheap at only $10. They also support the mbed platform with its online compiler, which makes it pretty easy to get started with. There's still a lot of room for improvement in the software, though.
While the Arduino did great things, I don't really see much point in continuing with 8-bit MCUs as hobbyist platforms. ST's Nucleo boards, for example, are far more powerful and very cheap at only $10. They also support the mbed platform with its online compiler, which makes it pretty easy to get started with. There's still a lot of room for improvement in the software, though.