Posted this question on the todbot page.
I'm suspecting power/ground/pullup issues on the i2c (using analog 2+3 for ground does seem odd/lazy, you're right), so that's the route I'll check next. Actually I have a standard 2d accellerometer I'll probably use instead of the nunchuck for the project I'm working on a the moment, but I'd like to know if i2c and digital pins can play well with each other, for future projects.
Yeah, i2c and digital pins play fine together "under normal circumstance". I've got 2 Lilypads connected over i2c, plus 2 serial devices, and a 595 controlling a bunch of LEDs as a visual feedback mechanism - and it works flawlessly.
Make sure you post a conclusion to assist others before they go pulling their Nunchucks apart.