The purpose of a transmission in a car is to reapply a load to the engine that places the engine back in its power band after the RPM of the spinning wheels has increased to a point that drops the load on the engine enough to cause it to overspin its powerband. This doesn't happen in a jet boat. Engine load in a jet boat increases with RPM and is not affected by the boat's acceleration, while engine load in a car decreases with acceleration.
Take a look at what a transmission does in a car. From a dead stop, the engine hits a certain RPM when you stab the throttle. As the tires start turning, the load on the engine drops, allowing the RPMs to increase.
Once the engine's vacuum rises back up as the engine load decreases, the transmission shifts to the next higher gear, reloading the engine, which drops the RPMs back down until the wheels pick up more speed and unload the engine again.
Props kinda do the same thing. As they move through the water, the front of them will unload, allowing the RPM to climb as the engine load drops.
The whole purpose of the transmission is to continuously re-apply a load to the engine that keeps the engine in its power band by shifting to higher gears as the vehicle accelerates and decreases that load.
Jet drives do this by default. The faster you spin them, the more load they apply to the engine. The load the engine sees is provided by the amount of water the impeller is trying to squeeze through the pump. The higher the RPM, the more water squeezed, and therefore the higher the load applied to the engine. This load is completely independant of the boat's movement through the water. This is why when you dump it to the floor, the RPMs immediately hit the max RPM the pump will allow it to no matter what your forward speed is. If the impeller size is ideally matched by the book to the engine, the impeller will allow the engine to spin up to its peak horsepower RPM and no higher than that. Jets act very much like a high stall torque converter. You stab the throttle to the floor, the RPMs immediately increase to the max that the pump will ever allow it to spin, and stay there until you back out of the throttle regardless of the forward speed of the boat. In any throttle position, if the throttle is held in one position, the RPMs stay put as the boat accelerates because a jet drive is a constant load regardless of forward speed. In all actuality, the pump and engine have no idea that they're moving anything, unlike a car or a propeller driven boat. As was stated before, a jet drive can be related to a high stall torque converter, a dyno or waterbrake.
Even if you were to use one to overdrive the pump at cruise to lower RPMs, in reality you would be forcing the engine to do more work at a lower RPM than you would be with a 1:1 drive. Example, let's say the pump is spinning at 3500 RPM, but the overdrive in the trans keeps the motor at 2000. Now it's having to drive not only the trans, but the pump as well. This means the engine is seeing a slightly higher load than it would normally see at 3500 RPM with a 1:1 drive, but it's seeing this load at a lower RPM. This would drastically drop fuel economy.
For the above mentioned reasons, IMHO a transmission has no place in a lake cruiser jet boat application.