I chose CommadFusion after being a Pronto PRO user/developer for many years. I played with iRule for a while, but the Fact that commandfusion integerated Javascript with their system on the iPad was the clincher for me.

The biggest issue with a sophisticated two-way control system like Commandfusion or the prontoi PRO (using it beyond just IR, but rather for IP and Serial two way control) is the other side.

You generally have little say over how the other side, the device you are controlling, operates and how well the protocol being used is documented.