Benyah,
The latest release,MyEclipse 2016 is built on Eclipse Mars 4.5.
If you are working with a higher version of Eclipse than the one MyEclipse is built on, you will see the newer workspace version warning when opening the Eclipse workspace in MyEclipse.
Though MyEclipse and Eclipse looks similar, MyEclipse extends the tools provided in Eclipse and integrates both proprietary and open source code into the development environment. There are several improvements in MyEclipse and you might not find the same in Eclipse to relate to.
I recommend you go through the tutorials in the MyEclipse Learning Center to get familiar with the wizards in MyEclipse : https://www.genuitec.com/products/myeclipse/learning-center/
Hope this helps. Let us know if you have any questions.
–Swapna
MyEclipse Support