How about having the serial monitor emulate an ANSI or VT100 terminal so we could use escape sequences to position text on the window. Maybe do color control and some of the other ANSI commands.
I use ANSI from embedded applications with the Arduino now, but I have to run Putty or other emulator on a separate serial port to do it now.
If we cant get ANSI on the serial monitor, I could do a serial switch to connect a second terminal with ANSI support. Use an IO pin, pulled up, so its high after reset. In this state the serial port is connected normally, but once the code starts it could set this pin to output, pull it low, and switch the serial connection to the secondary interface.