Running a ship engine with a long stroke (to increase torque) serves to reduce stress on the parts and increase lifespan since these engines have very long life expectancies.
Also, you are correct that the lower rpm engine would deliver more efficiency but not necessarily because it is larger/runs slower. It is more efficient because a smaller engine running at a higher rpm would have to work harder to generate the same power to move the ship and its load and would have the undesirable side effect of sacrificing longevity.
Theoretically, the 14-cylinder Wärtsilä-Sulzer RTA96-C could be even more efficient if it were instead a gigantic single cylinder. There must be some other engineering or economic limitation which prevents us from manufacturing 25,000 liter cylinders.
edit: example: http://en.wikipedia.org/wiki/Square-cube_law#Engineering_exa... "Watt recognized the problem as being related to the square-cube law, in that the surface area of the model's cylinder surface to volume ratio was greater than the much larger commercial engines, leading to excessive heat loss"
edit2: There is also a square-cube law with aerodynamic losses related to piston speed (how fast the air gets sucked into the engine: "pumping losses"). The slower you spin the engine, the lower your pumping losses are. However, I believe this plays a smaller role in affecting efficiency than the heat losses. (also, this engine is turbocharged, which changes things a bit).
Furthermore, in order to obtain the same level of torque in a single-cylinder that a multi-cylinder engine creates you'd have to account for the power generated per cylinder.
In the Wartsila RTA96C you have HP up to 109,000 (rounded) and torque up to 5,600,000ft-lbs [1]. These #s are for all cylinders. Assuming it is the 14-cylinder variant generating this power and you want to reduce this down to a single-cylinder package then you can easily deduce that the displacement would be around 25,480 liters (mentioned elsewhere in this thread).
Assuming a stroke to liter ratio of 1.374mm/liter (2500mm stroke for each 1,820 liter cylinder) you'd end up with a 35,009mm stroke for a single-cylinder engine vs. a 14-cylinder engine. Since there are 25.4mm in an inch that's a 98-inch stroke for 14-cylinders vs. a 1,378-inch stroke for a single-cylinder or an 8-foot stroke vs. a 114-ft stroke.
Finally, since you'll need a piston many times larger than the current setup for a single-cylinder vs. a 14-cylinder engine then you can imagine how much mass you have moving which can do some serious damage if it becomes unbalanced. Also you'd have an engine that instead of being long and relatively low is now very short and extremely tall (not something you want in a ship where capsizing is a very real concern).
[1] http://en.wikipedia.org/wiki/W%C3%A4rtsil%C3%A4-Sulzer_RTA96...
It's amazing to think how slow the pistons move on this engine. At 87 RPM, it would take a little less than a second for the piston to complete a cycle. Compare that to your average automobile where the piston completes 50 cycles every second (at 3000 RPM).
Does it burn more fuel to run a small engine at higher revs, or a big engine at lower revs?
The only other thing I can imagine being a factor is torque. Do low-rev engines have higher torque?