Longer stroke adds more stress on everything at same RPM.
Friction isn't higher for bigger bore than longer stroke.
If anyone has ever looked at some of the high power vehicles for racing, all have bigger bore than stroke.
If really comes down to, space and application. One might do shorter stroke to save on height of engine, or longer stroke to save on width of engine.
For application, you will see F1 engines that rev very high and make power are oversquare. For trucks, you normally see undersquare.