I guess hard-coding everything so it cannot display Arial is completely out of the question.
I'm one of those who worries less about the choices the publisher or device programmers make than how incompetently they implement them.
I generally prefer ragged right on ebooks because its harder to do it disastrously badly. Full justification doesn't seem to have a middle ground between perfect and "Oh My God that's terrible!" I also work with manuscripts a lot - and those are usually done ragged right.
I also prefer a serif font.
The rest I can deal with so long as it doesn't get in the way of the reading experience. I prefer indented paragraphs with no line breaks between them, because it makes it easier to show scene breaks, and doesn't make dialogue look funky.