Bill,
MyEclipse 2016 CI is a fresh installation and is on a different level of Eclipse than MyEclipse 2015 CI.
MyEclipse 2015 is based on Eclipse Luna and MyEclipse 2016 is based on Eclipse Mars.
You will have to configure the MyEclipse 2016 by installing the required third party plugins like Subclipse.
Please ensure that the version of the plugin being installed to MyEclipse 2016 is compatible and works as expected in Eclipse Mars.
Hope this helps. Let us know if you have any questions.
–Swapna
MyEclipse Support