With a more oversquare engine - that is to say a larger bore and shorter stroke for (nearly) the same cubes you will ALWAYS have the potential for more horsepower than an engine with smaller bore and longer stroke. Not only does a short stroke / big bore engine breathe well because of BIGGER VALVES can be used, it also has slower piston speeds and less rod angularity (read less motoring horsepower consumed). That is why the trend throughout automotive history has been to evolve to shorter stroke engines. For instance, our beloved Offenhauser Indy engines of the '30's, '40's, and '50's were surpassed with the high winding Indy Ford V8's of the '60's. It would be very naieve to think that any torque advantage gained by a longer stroke could not be more than made up for by overall gearing increases in the final drivetrain.
"But wait," you may be saying now, "the newest automotive designs are moving back toward longer stroke engines." Not as oversquare as in years gone by. That is chiefly due to emissions constraints and the wish to minimize hydrocarbon formations and get a more concentrated, faster burning engine design. Emissions driven, and, yes, also because front wheel drive East / West applications try to reduce the length of the block assembly. I think engines destined for high performance applications will still have to maximize the bore area to take advantage of more breathing potential.
