Great idea. Yeah, that could be done.

First pass would be to bundle the LEDs based on their type - just change the ordering from an ordering based on physical position to an ordering based on the logical meaning of each connection.

In the second pass, you could have a separate LED bank with LEDs marked USB3, USB2, etc. Hook those up to a couple of logic gates so that the LED turns on when it detects the USB3, USB2, etc. configuration.