Welllll, that is a deep subject not that easily dismissed. Generally that larger bore is also associated with larger displacement. No for a fair comparison, engine displacement need to be kept constant, which requires a shorter stroke. Then we open a can of worms as the CR needs to be held consistent. Then there is whatever contribution rod to stroke ratio has on the outcome. Then in all likelyhood the cam needs to be specified for each combination. Now in a racing application the large bore, shorter stroke combination will likely make more horsepower. For mainly street duty, the smaller bore, longer stroke combination is probably a better choice due to the potential for greater torque.