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The samples still need to be updated. This updates the built-in copy of React. The MVC Core sample was updated to support PropTypes and ES6 classes, both of which are required for React 16.
CommonJS imports are still not supported with built-in babel. I'm not sure how many people still need that functionality since compiling the client + server bundle with webpack ahead of time is a pretty stable alternative. So, it may be worth it to just deprecate on-the-fly JS compiler and move ahead with webpack-only builds.