Arduino + Raspberry Pi Thermostat and Zone Control -- Need Guidance

I'm looking into the same thing - my thoughts so far -

My Questions to this Community.

  1. What pitfalls am I missing? Will I destroy something??
    I'm thinking of leaving the main thermostat in-line with the new controller - maybe set to 80 degrees?
    That way if the new controller fails in some way, it won't keep the heat on.

  2. What is the best way to do R-Pi <-> Arduino Communication (uART,Serial, RS-485, IP, etc)
    i2c ?
    http://blog.oddbit.com/post/i2c-on-the-raspberry-pi