I think this is a deal breaker for a lot of people.
It's gotten to the point now, I think some people think RT stands for Reply To.
True, you don't have much room at the end of the tweet for your reply, but most people will just add a simple "LOL Yeah!" or something like that to the end.
This is the main reason I recently pared down my list of people that I follow - I just don't want to see all the personal conversations that other people are having.
More proof that users will just do whatever they want. People didn't use @Replies or Hashtags the way Twitter expected that they would. It's the same for RT.
You can put the comment in your next tweet and use a simple acronym at the beginning to reference what you are talking about... RTLRT (regarding that last retweet).