We've solved some of the practical problems you've described. The new C# compiler Roslyn makes determining relation fairly trivial, something that I'm assuming proved difficult in Clojure(script) and Javascript.
Many of the other issues are user interface/user experience problems that are better demonstrated than explained. Unfortunately, our demo isn't quite polished yet. We're showing it off at our school symposium in mid-March, so we should have something to show before then.
Would it be alright if I ran the demo by you when we finished it? Much of our inspiration for the idea came from CodeBubbles, Code Canvas and the original Light Table demo, so it's interesting to hear that you've decided against it.