In the same way that Twitter ditched "replies" for "mentions", they
should ditch the concept of a reply to a tweet, and instead let people
"attach" or "refer" to a specific tweet, which would then be included
along with the new tweet.
This fixes a number of different problems.
1. It handles all the situations that RT is currently being used
2. It gives people a full 140 characters to respond or add their own
commentary to another tweet.
3. Conversation threading, which is currently a total mess, is now
much more explicit and will probably even work.