I've worked with both ways, I much prefer to use System properties to define color and linetype of the piping as opposed to filters. There are some drawbacks, namely that whenever others link the MEP model, it keeps those colors. I always have Architects asking me why my pipes are blue and red and how to turn them black and white. Another quirk is that most Plumbing fixtures, air terminals, mech equipment etc. will inherit the system type view properties unless there is more than one system connected. For our print views we print in color to show revision clouds, titleblock etc. in color, but all the elements are black. To do this I create a filter for all MEP equipment and override the color to black. I also have a separate filter that keeps the linetypes as Solid for all equipment and fixtures. An easy way to convey this to other disciplines is either have them create the same filter in their model, or create a view with that filter turned on that they can use as 'linked view' in their model.
Using only filters to control linetype is frustrating when users need to add additional system types or when using a view that doesn't already have the filters loaded. However, as others mentioned, it is good practice (imo) to keep those 'layer' filters available to quickly toggle visible system types for things like riser diagrams, domestic vs. sanitary piping floor plan views, section views when designing, etc.
