I don't go for aorangi's cylinder area theory of piston friction much. I tend to favour jkm333's piston ring contact area idea. Friction is supposed to depend on coefficient of friction, perpendicular force, and contact area. The cylinder area idea is a bit like multiplying the width of a tire by the length of a journey, so I don't think the number it produces is that relevent although I'm not saying it is altogether irrelevent.
So bigger bore will give more of jkm333's piston ring contact area. That works against bigger bores.
Working against larger stroke engines - I've just noticed its the same name - we have jkm's piston speed. Like he says, answering his own question, if it was just volumetric efficiency, they would be chasing that exclusively, but in practice, they are seeking to reduce piston speeds, among other things. Kinetic energy of the pistons is ½mv². As RPM increases, piston speed increases and piston kinetic energy increases. You could calculate an RPM where the whole power of a cylinder combustion was used just to reverse the motion of the piston ,and there would be no power for anything else at all. So high piston speeds are bad.
Increasing the stroke increases the loses reversing piston motion. Increasing the bore increases piston ring contact area and so presumably piston friction.
The ideal bore to stroke ratio will be when the loses are a minimum: it will be a delicate balancing act between these (and other) conflicting loses. It cannot be as simple as saying the ideal ratio is X:1.
For example, if lighter piston materials could be found, then piston kinetic energy would reduce and the balance might tip in favour of higher piston speeds, ie longer stroke.
If engine cooling were improved, cylinder temperatures could drop: piston friction would be reduced and the balance might favour wider pistons, ie bigger bore.
To come up with an ideal bore to stroke ratio for a particular engine and particular operating conditions I think you'd need to have an idea of functions for all the bore to stroke ratio dependent loses, eg my two simple examples, piston friction and kinetic loses and choose the value that minimises these loses, ie maximizes efficiency: power if you prefer to use that word, but I think the word encourages waste!