Waypoint scripting would be counter to how ATC works. The challenge is remembering your plan for each plane and mentally queuing up the instructions you need to give to pilots.
Except that real ATC can indeed give instructions of that sort. It's not so common for terminal environments to give really long clearances during approach because the pilots may not be ready to copy them down right away, but instructions like 'fly direct WAYPOINT, cross WAYPOINT at or above 5000 then descend at pilot's discretion to 2500' are common enough a bit further out.
You could in the terminal based atc from BSD games. Great fun.