I’ve changed all my native email apps to sort conversations “newest at the bottom,” like Gmail.
When I read an article on the Internet, or anywhere, I read it from top to bottom. Why, then, would you read a conversation thread from bottom to top? Is the UI optimized for reading while hanging upside down from the ceiling? That sounds like a 5% case to me at best. 🙂
Take the First 
Just like email quoting was done newest-on-bottom when sending emails prior to 1995 and for Usenet posts. Somewhere around 1995 somebody screwed up the defaults, forcing us to have to read long multiply responded to emails upside-down from bottom to top, aka Top Posting style. I think it was the first Netscape mailers that foisted this abomination on us, soon copied by everyone else who had no knowledge of how to make email reading efficient for the recipient.
Although, it is also possible that the blame for this may actually lie with Microsoft mail programs. But I seem to recall that Netcsape was the first offender.
When reading an article I haven’t read it before so it’s all new content, we read top down. With an email, I’ve likely read all that it’s in reply to (or wrote it). So the new content that I haven’t read is placed at the top; and is quick to read; and easily fetched and shown as the preview. This is especially important when viewing on a mobile device where bandwidth is a costly (and potentially slow), and emails aren’t always fully downloaded when you start reading, but pulled down a bit at a time.