Not sure if any of this has been mentioned/requested before, but I think two things would be great to add...
First off, proper valve timing. In stock it looks like all cylinders are synchronized, whereas in reality each cylinder needs to have the valve timing shifted 120* from the one before it. Basically, if cylinder No. 1 is at Top Dead Center then No. 2 should be a third of a revolution before TDC, and No. 3 should be at two thirds before TDC, and Nos. 4-6 are a mirror-image of of 1-3.
The second idea is to seperate the animations for the left and right engines so that when one is charging the batteries it can be animated at full speed, while the engine driving the ship is still animated at telegraph speed (preferably with independent sountracks for each engine, too, but that might be harder to implement).
A smaller problem is that in stock the port-side shaft is stalled when charging batteries, but the starboard engine indicates full speed in the engine room, control room and conning tower. Either the shaft or the gauges need to be swapped...