In AutoCAD based products you have the ability to see things that won't plot through the use of No-Plot layers. Revit doesn't have this capability. In the MEP world it is imperative that you have the ability to see the other disciplines without plotting them.
One way to handle the situation is to create separate view templates for modeling and for plotting. Users must be sure to switch to the plotting view template before plotting which can be done relatively easy by selecting all the appropriate views in the Project Browser and right clicking to apply the view template.
A little sexier solution can be achieved with some knowledge of families and the detail level view control. In Revit Architecture using detail level shows the appropriate amount of detail at different scales in objects like walls. On the MEP side of the fence view control is pretty much only used to switch from single line pipe and duct to double line. When creating families you can set the visibility of electrical plan view symbology to only show in Course and Medium. Then set mechanical families view in Medium and Fine. Electrical and mechanical users can design in Medium detail for coordination then switch to Course or Fine respectfully for plotting. I also override the colors of the alien equipment so their presence is painfully obvious.
For this to work, you will have to visit every family that is not shared by both disciplines. A fun activity for implementations maybe? It's more work on the back end (for you), yet much easier for new Revit users to understand. It's your call until Autodesk addresses this requirement to good engineering.