I planning a similar hook-up when my Pi has been baked and posted.
The ATmega will be acting as a I/O pre-processor for the Pi, doing all the background stuff, and also acting as a firewall in the even something goes *phut*. ATmega328 is far cheaper and easier to replace than an ARM!
Hopefully it will also be able to put the Pi to sleep and wake it up if something interesting happens it should be told about.
On the subject of voltages, the ATmega328p will happily run on 3.3v, even at 16Mhz. Officially this is out of spec, but I've got several boards which confirm there isn't a problem, and the ATmega328p based JeeNode boards are all run at 3.3v and 16Mhz.
Running at 3.3v gives you access to other fun things, such as the RFM12B radio module and a host of I2C toys.
- Yes Soren, I'm watching you SPI based RFM12B thread
http://www.raspberrypi.org/phpBB3/viewt ... f=9&t=3404