I try to always maintain the following:
1. Forward motion if the rope is out
2. Little to no slack in the line if I'm waiting for a boat to pass or the rider to say "hit it"
3. If the riders done, I circle around so that the rider can get ahold of the rope/handle. Shut off the engines. Then pull the rope/rider in, coiling the rope as I go. I NEVER leave the rope in the water by itself. I pull it in with the rider.
4. Next rider gets ready on the swim deck, grabs rope handle and jumps into the water with the handle. Then I start the engines and idle away from the rider as the rope uncoils on the swim platform. If you coil the rope properly, it will pay out on its own. This also prevents fingers/arms/etc of a "rope assistant" from getting pinched by the rope.
BTW, pulling from a tower makes this so much easier because the first 10'-15' of rope is naturally lifted out of the water. I don't ever have the engines running if I see the line coming off the tower and next to the boat.
The above steps have pretty much eliminated sucking up ropes while I'm operating the boat. However, my wife does drive every now and then too