I seem to remember something being said at the announcement that they improved the display algorithms [perhaps font rendering? eink controller firmware?] in some way... I can't seem to find it now, but perhaps that could account for some of the differences?
I can't put my finger on it, but there does seem to be a notable difference between the way that the Kindle, Nook, and Sony (all using Perl displays) write their text to the screen, and no matter which font I select on the Nook/Sony I still have an unexplained subjective feeling that the Kindle 3 rendering is easier (for me) to read. I haven't seen a Kindle 4 yet, so I can't comment on them.
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