Seems like an old thread but i'm about to do the same thing.
I'm using an Arduino for controlling some components, and i will have an RPI that's connected to internet asking some REST-API:s about info and from this send 1/0 (true/false, whatever you wanna call it). Something like "hey arduino, you should do your thing now".
I was in the same thinking as above (using pins), but then i found this article:
I like the solution of using USB ports - no need for resistors or level shifters. The code on the RPI is python, another lib will do no harm. 
Anyone tried this solution?
Pros/cons?
Question: Arduino can be powered bu both DC-input (and on pins..?) and the USB. Will it run on the USB power from the RPI or should i connect the Arduino to DC-input?