While I don't buy into the view that reading on an LCD is bad on your eyes, I do get some minor discomfort if I check my email on my iPad right after I wake up, but once my eyes are adjusted to the light again, I can read on the LCD screen of the iPad for hours on end and have no eyestrain.
That said, reading on e-ink is a more pleasurable experience for me when reading novels. It has nothing to do with comfort though. It's just a more mentally pleasant experience for me.
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