I don't have much time to debate this, but two points: 1. If a client is making users jump through hoops to reply to a specific tweet, the client is doing it wrong. Twitter.com does an excellent job making it easy, as do the vast majority of iPhone clients.
2. Adding another setting to control whether or not you see auto- linked reply links (as Simone proposes) is too complicated. I dare you to try to explain what that setting does to the vast majority of users. Most of them can't figure out what the current replies setting does. The end of auto-linking was a fantastic change for two reasons: 1. it keeps everything simple (no new settings or flags or functionality), 2. it allows developers to trust in_reply_to_status_id, paving the way for some *really* fantastic stuff down the road. Loren
