Ideally, Mr.Bauman is right (as he often is when talking about a perfect world that doesn't exist). The proper place to hold a train is usually in a station. However, in the case of holding the R, for example, there is a V train somewhere behind it that has to stop at Queens Plaza and then go somplace that the R isn't going (that is to say, via 53rd Street). Of course, that doesn't adequately explain N vs. W...
Speaking southbound only here (don't feel like looking at the northbound, but we're not talking about it anyway): With respect to merging conflicts between Q/Q and W trains in Manhattan, they've been worked out through holding at Times Square. Same goes for N vs. W in Downtown Brooklyn, where trains are held at DeKalb Avenue (on the "bypass" in the case of the W) where necessary. There don't appear to be any conflicts between M and N/R trains going through Montague Street or between M and W trains at Ninth Avenue.
As to which timepoints are listed and which aren't, any station (or other landmark) along the route can be a listed timepoint on the official timetable (as I understand things). It's simply a matter of space, which isn't available on the R or W official timetables given all the other locations that ARE listed.
In short, the schedule represents what can be done with the number of subway cars and crews supplied by the Department of Subways, using the routings supplied by the planners (remembering that any one route we've spoken about here has to interact with several other routes along the way, and proper spacing between trains has to be maintained throughout the process). Is there room for improvement? Probably, but it would most likely require resources that the operating divisions do not have.
David