I'd love to see cap files replaced with something along the lines of an IDE style project folder. The general project info would be in an XML file (settings, lists of objects & plugins, etc.). Everything else would be pushed out into sub-folders (images, music, data, layouts, events, scripts, etc.).
C2 could then have a function to bundle entire project folders into zip based caps for sharing, but still giving teams the ability to collaborate on project using CVS systems. Event sheets, layouts, object settings and families could all be created using XML files, meaning you could even make small changes to projects using notepad.
Unity3D has something like this, whereby dropping a file into a project folder immediately makes it available in the IDE. A really nice system, IMHO.