Extensible programming
Rereading Greg Wilson's article (Extensible Programming for the 21st Century) and a few others in the past weeks, has made me think a bit more.
I'm don't think that the underlying representation matters as much as having a common tool to manipulate it. In the case of Java/Eclipse (or C#/VS .NET) - storing the results (the code) in text is fine. What we need is for Eclipse (or MS) to expose the asbtract syntax tree to the various plugins. In many cases these plugins will bypass the text editor and display the program in their own way. I think this allows us to make the leap to the next generation tool without having to replace the infrastructure (ie new source code control systems etc.)
Update as Trey pointed out - by expose I didn't mean readonly - I meant expose for and allow for modification. Thanks Trey.