The effort is great. Kudos to the team at Twitter for trying to tackle this.
Unfortunately, from my view, Project Retweet uses a sledgehammer to drive a nail. The simplest solution is going to be the best, and I think the current changes are complicated and confusing. I agree with some of the other comments; tracking the original tweet id in a single field would have been sufficient (retweet_of_status_id). I like to comment on my retweets. Project Retweet actually increases the number of tweets that I'll have to post (one to retweet and another to comment). Project Retweet encourages thoughtless copies of tweets. While that happens anyway, there is at least a small barrier today. It appears that too much work has already gone into this project, so it looks like we're moving forward. With that in mind, I hope I'll be proven wrong.