As can be seen from your photo, the default font has changed between the two versions. This could explain some of the differences, the linespacing in particular.
I'd be curious to know your impressions when that change is abstracted; would you mind trying with an EPUB that incorporates a font (e.g. Darwin's Journal of Researches, available at
http://efele.net/ebooks/livres/000177/index.html; pick the "epub" version, not the "epub-").
As for the aggressive hyphenation: have you seen if there is a reading option to turn it off?
Thanks in advance,
Eric.