I'm going to have to say Kindle over iPad, but it has nothing to do with the visual qualities of the screen. I prefer long battery life, compact, and light weight devices. On the other hand, the difference between the screens (for reading formatted text) is arginal.

I think the solution would require the collaboration of a physicist, a biologist, and a psychologist. There may be no difference between a transmitted and reflected photon, but there is a huge difference between a transmissive and reflective display. There is the intensity of the emitted light, compared to ambient light, as you mentioned. But I'm curious as to how other properties may factor into our vision. LCDs emit polarized light and the spectrum of the emitted light will be different from reflected light. I don't see how that would change anything since our eyes can't detect polarization and are very poor at judging the spectral distribution, but I'd want to ask a biologist to be sure. Of course it may also be in people's minds, thus the psychologist.