How do you know that the problem is that too much power is being drawn from the USB?
If you are supplying 12V power to the Mega, and the 5V regulator on the Mega is working properly, then the system should draw no power from the USB. So if your diagnosis is correct, the voltage regulator on the Mega is probably faulty, or overheating due to overload, and the power draw on the 5V rail is too much for the USB port you are using to provide.
One thing I hear people doing that is a very bad idea IMO is to run a full graphics controller exclusively from the 5V rail. The 12864 displays used in these controllers take around 100mA of current for the backlight, which adds 0.7W of power dissipation to the voltage regulator on the Mega. My advice is instead to power the backlight from the 12V supply via a 100 ohm 1W series resistor.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].