Here I will try describe my vision of the future in Joomla! Some opinions, some ideas.
Let start this discution with the main idea. In my vision Joomla! would have lot of
Applications. At this point, we can use the framework to create new sites(multi-sites), ecommerce, blogs, forum and more. But now your have think but today we can construct ecommerce components, blogs, etc. Yes we now, but in case of Ecommerce application inside a component is very complex for future administration of code, the evolution of ecommerce application if you dont think you will got a problem in the future.
I think the for ecommerce application we can construct a new application like "Administrator" in Joomla! and we have extensions of ecommer to control some functionalities like wishlist, customer, products, attributes, etc. separed by extension(components).. this way we have e better structure for construct applications.
Today we have site application and inside our extensions(modules, components, plugins). If in my vision we decide to start a new application for example ecommerce: I need to copy com_content and put inside my application. This is bad for maintence, re-use, security, etc. In my mind in future we extensions dont inside the application but like a service and you call this service and use anywhere if you need. We can share services like: Extensions(Component, Modules, Plugins), Email, Autentication, Login, etc.
So I will sugest this structure based on this Idea:

App - applications folder
Dsl - Domain Specific Language (Maybe I will change)
Extensions - We put all extensions here like our repository of extensions all applications can get any extensions from here. (Modules, Plugins, Components). I will write more details..
Js - Inside we have Mootools folder, Joomla folder(js used in cms) and if want we can have more js things
Languages - All languages here
Lib - Repository for frameworks and libraries
media - Media services
Will finish for here I will write more soon...