Is it not the case that for sensors of the same generation, of the same physical size but different resolutions, that outputting still images to the same dimensions (i.e. printing or viewing the whole image at the same size), none of the disadvantages of smaller pixels are visible? I.e. the issues with diffraction, motion blur, etc are only greater with a higher resolution sensor when viewing 100% because you are magnifying them more? I take your point about losing a little bit of light gathering area by subdividing the sensor more but in practice that seems not to make a noticeable difference. A lot of people seem to cling to the belief that 'lower res = better high ISO' but there's precious little evidence of it, for stills.
With regard to phone cameras, surely the big issue is that the sensors are very much smaller, so they gather much less light overall.