michael said:

as I have had multiple comments from our readers that they LIKE not having such boringly justified right margination, as it helps them better keep track of what line is next.

and the beauty of a good viewer-app is it lets each user decide.

As for the footnotes, I still agree with those who want an appendix containing all of them, rather than having breaks between pages contain them. 

it doesn't have to be "either/or" with e-books, it can be "both".

I like this with paper books, and even more with eBooks, as it is trivial to switch from the text to the footnote and back again.

i think it's even better to have both displayed at the same time; no switching required.

I'll leave the pagination and margination issues to reader choice as their own personal decisions, along with fonts.

i agree. -bowerbird