In my head the cut / paste thing could be resolved by making the rectangle selection static, then using a hotkey to move or rotate or copy, to those that have learned the hotkeys it will line up with how they treat individual components.
My understanding of software is sadly only C, so i guess i will have to throw some dollars there way, would love to see layout dependent calculations on the PCB side, e.g. import parasitics, you know the trace width, distance to ground plane, plating thickness, can specify the board material, etc, so a crude approximation could be brought in to compare one layout to another, e.g. add the RLC of a via, add the ground plane capacitance of a trace, I mention this because those parameters can be retreived using already understood math,