This might not be what you need but is some of what you ask for. If you can use windows then you can download a free copy of Visual Studio Pro for 3 years and subscribe to the Arduino Debugger beta team for a free software debugger.
The debugger allows you to inspect registers, variables and expressions on a running Arduino. It also comes with open source digital, analog pin visualizations. You can also extend the debugger by building your own Visualizations of any Arduino data.
It also supports updating variables and registers on a running Arduino. BUT be aware this is not a hardware debugger, it injects code into a temporary copy of your Arduino sketch during debug compile. Many people have found this debugger very useful but it is not a perfect solution.
