The obvious solution here is to not merge the whole thread into your email, instead including only the parts of the message that are directly relevant.
Wave seemed to me to be an unimaginative copy of other threaded comment implementations. The indentations seemed to waste valuable space on each page. Allowing anyone to edit anyone’s post seemed insecure. If I hadn’t known it was Google, I would’ve thought it to be a bad college project.
You should look at the git mailing list. They actually send patches via email using the git format-patch and git send-email commands and have complex discussions around some of the patches.