How to clean up emails when replying in plain text?
I haven't seen a good universal solution, but have found that by selecting only the bare minimum text I need to reply to, I can often get a clean, clear reply that doesn't need substantial (or even any) clean up when replying in plain text.

Sadly, the best solution for presenting these emails cleanly is a powerful email client like elm. BBedit, Safari's reader and Coda 2 are all in my toolchain for taking a complicated HTML document and thinning it down but it's awkward to send the text to a second program, operate on the document and then get it back into a reply using Mail. 

I wish I could serve you up a delicious cake of a plug in, but sadly, the Mail plug in scene isn't lucrative and this use case doesn't have a champion that's programming a better converter than the one Apple has provided.

Of the reviews of plug-ins, these are the best:


http://www.tikouka.net/mailapp/
http://www.macworld.com/product/collection/6866/mailaddons.html


And if QuoteFix won't work for you, you may have to program this yourself. It might do the trick by deleting trailing spaces, but without a sample of your mail in question, it's hard to tell.