Ring friction is high enough to tip the scales to a large bore short stroke, all else being equal. Thats the info from an engine design book used in the past at Cornell University. Narrower rings in use today may have reduced that some, but crank case windage will be higher with a longer stroke also.
Modern engines like the Ford Coyote 5.0 have a square bore/stroke arrangement to suit emissions. It gets real hard to keep a motor clean with a larger bore due to too much dead space around the top of the piston of a large bore cylinder.