Been wanting to figure out a way around this for ages. Here is what I've found. I know you asked a long time ago, but perhaps these links will help you or somebody else…
First is a simple script from John Gruber at Daring Fireball the script allows you to "bottom post" with the help of a bit of AppleScript and the help of an app called FastScripts. FastScripts costs $15 if you want to support the developer or need more than 10 scripts activated by keyboard shortcuts – otherwise it is free.
The second option is an app called QuoteFix by Roger Klep. It's a fairly nice plugin for Mail that gives you pretty reasonable control over how the message is formatted when you reply (my only complaint is that it won't leave a blank line above my signature, but I can fix that by adding a line to each sig. Pretty much painless. The plugin is free with a very low key request for donations.
Both appear to work with recent versions of OS X. I tested with Mountain Lion.
Douglas, it was kind of you to post that reply, but since the solutions you recommend apply to OS X rather than iOS, they don't really help the OP, who was asking about Mail on the iPad in this "Using the iPad" section of Apple Support.
All the same, it's good to learn about them.
Meanwhile, I join Shoshanna in her wish that Apple would let us set a preference for how replies are handled. I too really want my sig to appear UNDER the quote from the previous message.
Considering that she posted her question in late 2010, it's disappointing that Mail still hasn't been improved in this regard over two years later.
Can Mail.app be made to "bottom-post" replies to email?
