Without addons like you have with Catia...
Here is how I do it in NX. Manually.
I make sure both assemblies "Read Only"
Then I make a "new" file from a template and add the "old level" assembly to it. Change color to RED
Then add the "new level" assembly to it. Change color to GREEN.
I go through the ANT and uncheck any files that are the same (identical file names)in both assemblies and other parts not relevant to my project.
Then I use "Model Compare" to compare individual components.
Now this only works well with major OEMs who supply NX files. If its imported data, other steps may need to be taken to ensure things stay sorted out correctly. We've got a bunch of customers who never "rev" up files. occasionally we will get 4 engineering changes all with the exact same file name.