Sorry I should have expressed myself more clearly. A short stroke engine may actually be more efficient and has lower internal stress on the components. It tends to develop its maximum torque at higher RPM for several reasons, including the fact that it can have a greater valve size for the displacement (due to the larger bore). Because of lower stress on the components it can be made to rev at a higher RPM than a longer stroked similar motor. Most people building a race engine would favour an oversquare motor for maximum power developement.
A road car, on the other hand, requires good torque at lower rpm. Imagine the situation when you want to accelerate quickly or overtake without changing down 2 or 3 gears and revving the nuts off the engine. In this case an undersquare motor will tend to produce more torque at lower revs, this is partially offset by the inherent slower acceleration of the longer stroke engine.
In the case of the engines we are talking about the differences in stroke to bore ratios is not actually all that great and both engines are very efficient. Given the choice of the 2 litre Duratec and the 2.3 I would always opt for the 2.3 for a fast touring car. The extra 15% of capacity and the low speed torque characteristics make me wonder why Morgan never offered this as a choice. The 2.5 litre Duratec would even better suited. As the Yanks put it "There ain't no substitute for cubes" that is as long as you are talking about naturally aspirated engines.