Enterprise Architect 13 allows you to easily compare 'As-Is' and 'To-Be' models, being able to analyze a diagram to see exactly what changes occur at every iteration. Simply select the package or diagram you would like to change and use the Context Menu to 'Clone Structure as New Version'

Now you can make changes to subsequent versions without altering the underlying structure of the 'As-Is' diagram. This Cloning approach provides substantial benefits and allows you to take a snapshot in time of model development.
 

When you clone an individual Element, Enterprise Architect automatically prompts you to enter a value for the new version number.

This gives you greater control over the evolution and traceability of your overall model.
 

Represent Past, Present and Future without having to re-build the underlying structure for each repesentation.

Use the Insert Related Elements feature to automatically create a Traceability diagram that outlines each stage of the elements evolution.
 

Time Aware Models can use Diagram Filtering to highlight elements used in Past, Present and Future versions. This allows you to quickly determine which elements have been modified in each version.