Please find a new release of the sketch and javas as requested 6 months ago in this github thread https://github.com/arduino/Arduino/pull/1267 where now the java GUI offers much more sliders, checkboxes as well as LOG console directly communicating with arduino MEGA or DUE being the client
Many people have read your post, but I believe they do not understand yet the true power of this GUI.
For the sake of clarity to everyone: - there is a part which runs on Windows or Mac - this part is called the GUI - there is part which runs on the Arduino (Mega, DUE, ...) - and is part of the sketch - between the GUI and the sketch, there is USB communication (the standard one used by Arduino), and a proper protocol for exchanging data
In the Arduino sketch, you define what parameters you would like to use in teh GUI: - there are 12 sliders on which you can set the min, max and default values - in addition there are 6 checkbox controls - lastly there is a console text section Once you start your GUI, you get a default screen. Upon establishing the connection the Arduino (is just selecting the right serial port), the setup parameters are exchanged. From then onwards, you can adjust all your desired Arduino parameters LIVE from your GUI!
As an example, you can life-update the PWM frequency, or duty-cycle of any timer (you just program in the sketch what you want to get). Same with the 6 checkbox. This acts like an on/off switch, where you can command just anything to your Arduino. The console section, is to receive text messages from your Arduino, as you have programmed it in your sketch. Suppose you have a system programmed with a PLL, you could send a message to the GUI telling the "PLL is locked". Use your imagination!!
It's a very flexible thing. In stead of juggling around with adjusting the parameters in your sketch, reprogram and reload, you just do it live from the GUI. It's all Open Source for use.
just another note:
see also this tread, which takls about the porting the Mega timers to the DUE: http://forum.arduino.cc/index.php?topic=186389.0