Finally, you can now use ArduPilot Mega without ever having to touch Arduino! Michael Oborne's terrific Mission Planner will now check for the latest code online and load the firmware directly, with no Arduino compilation process required. I've updated the APM 2.0 beta instructions to show how to use it.
You can still use Arduino if you want to fiddle with the code, but most people won't need it at all. No need to even have it running on your machine!
Right now it only supports the default configuration, but in the next day or two it will allow you to choose other common configurations, such as Xplane simulation mode.