Air traffic control has a lot more things to deal with. There are scenarios like runway closed and all traffic has to be diverted. Loss of communication. Various emergencies. Weather changes. It's not just a question of 3D motion planning. Controllers in the tower also use their eyes.
In your imaginary system how is the software "tower" communicating with airplanes, using voice? I don't think we even have software that can reliably decode the variety of human voices over radio that a controller can respond to.
One can imagine a digital protocol to all airplanes but technology works its way really slowly into aviation.