Is i2C more or less robust than GPIO?
Here are a few things to remember:


You should have a ground connection between the RPi and Arduino
I2C was meant for really short distances on a printed circuit board
Arduino runs at 5 Volt logic levels and RPi at 3.3 Volt logic levels - you need a level translator between them to make that work.


If the RPi and the Arduino are not far apart, I would say less than 1 foot (30 cm) and you have the grounds connected between the boards, then it is a software issue. I2C is meant for short distances any anything longer than a foot puts too much capaitance on the wires and starts causing unreliable communication. I would not even use it for more than a few inches unless it was on a circuit board where you control the capacitance.

I am assuming your using the Wire library on the Arduino side. On the RPi side I would use the the Adafruit I2C library for the RPi as I have had success using the library to communicate with I2C sensors listed on their site. Here is the link:

Adafruit RPi I2C Tutorial