We can go back to flags
Or we can go back to lights
Here's my idea: Have six spotlights, three red and three blue that point at robots of the respective color. These spotlights follow the robots throughout the entire match!
But my preferred realistic idea is red and blue lights on the robots. But this time around maybe add some RGB LED strips in the KOP and make it a requirement that the robot have the strip(s) surround the robot on all sides. Since the strips are RGB, any teams can shine their own colors when off the field.