No modern mail reader does well with plain text email. Most likely it doesn't wrap properly on small screens (phone) for example so they are scrolling horizontally. It doesn't wrap properly on large screens (they are seeing a narrow 80 or less character wide tower of text).
If you are bottom posting most likely the recipient doesn't even scroll down and see it.
If you are top posting plain texts probably break the ability for the reader to collapse the rest of the thread underneath and scatters > characters all over. The mail reader is probably choosing some nasty fixed width font.
I say this as someone who spent too many hours trying to send email with emacs and being embarrassed by the terrible results. In the end you need to hack in some markdown to html converter and write all your mail in markdown if you want any chance of a readable email.
Mutt, emacs, whatever. They are fine mail readers. But you really can't write actual professional emails in them anymore.
I am obsessive about formatting emails, and the `par' formatter is the only one I've encountered that can intelligently work with indentation and quoting characters:
Vim has a basic formatter, and I'm not familiar with Emacs' tool, but I'll bet it's not as good as par.
EDIT: Your point about reading plain-text email on mobile devices is very true, of course.