I wonder if creating a whole new cms using WP as a basis is the best way to go. Update the php core, phase out anything related to WP, but the big one is the editor. The best editor I have used in a cms is the JCE Editor (an extension for Joomla) which eats WP for breakfast, lunch, and dinner (with snacks in between). Perhaps make a deal with JCE. This editor also provides an amazing media management system that also kicks the butt of WP. As for widgets, give serious consideration to being able to hide widget titles, publish widgets to select pages, a field to add a class...these are things that should have been part of widgets without third party plugins.