A civilization uses the sci-fi staple of space gates to get around between systems. These gates, for our purposes, are big, round and very much not transparent; think the star gates but huge or the gates in the X universe of games. You can't see though them, we will assume they have a frequency shadow some what like deep water.
The civilization has a huge range of ships, some tiny like cars and some colossal ships that only just fit through the gates. A system is doing really well, traffic is up a huge amount on last year, but there is a problem. The accident rate is also up.
How do you stop ships popping out of the gate directly in front of another ship, causing an accident? However, efficiency is very important. We don't want to limit the gates to one ship at a time in each direction. However, if one of the really big ships is coming through it is necessary to stop all craft from the other side. It is also important that ships keep a minimum safe distance between each other. When a ship enters it leaves in the same place on the other side. The ship has to be entirely inside the portal before it starts coming out the other side. Travel time is near instant once inside the portal. Ships enter and exit at the same speed.
Bear in mind that it is hard for the two halves of the gate to talk to each other, deep water is hard to transmit though (though not impossible). I would like to not break the Nyquist rate limit here. Some other method of communication between the sides is possible. I had a slightly crazy idea of using ping pong balls to signal a ships impending arrival while thinking about this.
Ships not following the proper protocol will be dealt with by law enforcement, for "Reckless endangerment of life in control of a ship" or some such law.
I'm looking for a system that provides the best bi-directional through put of ships and doesn't cause any one to sit in a queue for hours on either side of the gate.