"both 5V and 3.3V logic, meaning you can use pretty much any part without level shifters"

Are you sure about that? It can provide different voltages in different pins, but the ATmega32u4 will work with 5v logic (if it is like the Leonardo, at 16MHz will be 5v), so you're in the same situation really and you won't be able to use a lot of 3.3v logic ICs without a translator.

I can be wrong though and this one operates in a different way, but doubt it.

EDIT: ignore me, the page says it has 3.3v logic pins.

EDIT 2: right! they're provided by the Sitara processor and not the AVR, so I wasn't 100% wrong after all ;)

See: https://github.com/CICCIOSGAMINO/arduino_TRE

also: 7 hardware PWM outputs (the Pi has one)

You can sort-of do analog input-output via the audio ports on the pi, right?

Cool, didn't know that.

Seems like the hardware has to be modified and it only supports 0-1V though: http://raspberrypi.stackexchange.com/questions/8757/using-pi...

PWM is useful because that can be used to drive servo motors and brushless DC motor controllers and other gadgets. It can't be easily replaced with analog output, e.g. from audio ports. OTOH, audio ports are a lot more useful if you need actual analog output.

PWM could be done with an op amp, a triangle wave generator, and a handful of discrete components. It's how the front-end of a Class D amp works. Would definitely be more of a pain in the butt than having pwm ports directly, though.

Pi 1 B+ has 4 USB ports as well.