I would definately get the optional serial port so you can access with your computer.
I have to agree with you here. One of the greatest advantages of using a controller is that you can record the pH, temp, and depending upon the model of controller, several other variables. By recording the values over a long period of time, and by recording them every hour or so, you get a long term view of your system.
This makes it possible to spot problems long before you'd notice them by more conventional means.
In the case of the Aquacontrollers, you don't necessarily need their software, but it makes using the controller easy. You can program most functions and record and chart readings all via windows.