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No, I don't agree. Js is not a module but a collection of .js files.
Lang could be in core, but I think language (content) should be separated from core (logic).
System should be all logic that is used in multiple parts in the site (basically the current system folder without core and lang folders).
core != system, as core is only a parent folder for a bunch of other folders (as it is now) each containing a specific core module for the site, while system is only a collection of globally used files (functions.php, common.php etc).

Keep in mind we use the Model-View-Controller architecture, which basically splits code (files) into three sections:
- Content (database data and language files)
- Design (skins)
- Logic (core/modules/plugins)

In the case of Cotonti, it's preferable to have subsections in Logic, to separate core code, modules and plugins.