Tastes differ!
I very much dislike the way of the epub firmware that it doesn't set any margins automatically and I really like the mobi firmware for setting these margins! I think with margins a book page looks extremely better, but that's of course a personal opinion.
To get to a more "impartial" ground: the mobi version is very, very stable and it offers the additional advantage of using a dictionary, but I don't know if this is important for you.