The first thing to consider is that a diagram is not "the model" but a view of the model. Only create diagrams that communicate specific aspects of the model that are important to you.
The "spaghetti mess wiring" diagram that shows every class in your system can only communicate one thing: that your model is complex. As such, you don't need to tidy up the wiring; I'm sure the diagram communicates the complexity fine as it is ;)
If you want useful diagrams though, I would suggest identifying the most important classes in your model, create a diagram for each, drop the class onto the diagram and right-click->Add->Related Elements (I think that's what the command is called). You will end up with more diagrams, but they will be focused on what is important.