Domain models are often very complex after some development time. Even if you split it up to different modules. I think there is a easy to implement way to improve the way you can organize your domain model and that's to add layers.
I guess it's relative easy to develop, because it's only a visual thing. Make it possible to move entities to layers you can define yourself in a model. It would be very useful when each layer has his own tab page, but showing layers via a multi-select option would be also nice.
What do you think, would it be helpful to organize your models?
Highlighting would also be a very nice feature! I also like your first sentence… Because that's exactly the reason I'd like to have layers.
Layers will make you have to organize them even more. Which entity needs to be in what layer, so I am not in favor of that, but automatic layers would help. Highlighting and bringing to front of all elements related to an entity that you click would help.