Here's my take.

Semantic Program Storage

Programs are stored as datastructures, not text files. The programs are projected into the editor via transforms. Users can pick their favorite syntax -- like a skin.

Plus, you could have projections for graphical representations of the code.

And, the code is essentially a revisioned database. It can be queried efficiently, viewed as a graph, etc.

Code Views

Subsets of the codebase can be grouped together into a "view" which accomplishes something useful.

Wiki-Style Inline Documentation

All documentation is cached locally, but can be edited, and synced with the web.

Live Scratch Space

Reinteract or Subtext-like.