For best power out put, the biggest bore shortest stroke for the same cubes always comes up the winner. Simply less friction from rings, for starters. The rings are about 50 percent of the total resistance to rotation in a shortblock.
A larger bore/shorter stroke has much less total drag. Generally more room in the pan area to absorb windage from the piston motion and rotating assembly. Also makes for less total rotating weight and less valve shrouding.
Look at the modern prostock- 4.6+ bores less than 3.7 stroke.