You're correct that I have made a couple mistakes here around the JMZ relationship. First is that the Z would also be express relative to the M train between Marcy and Myrtle. I didn't realize that the J is also express relative to the M train over the same portion at rush hour. This would cause the M to surpass the R as the most local train, because it would now be local relative to six (!!) trains.

Part of me is inclined to say I'm not including rush hour service, because then you also get oddities like the occasional N train running on the Q line and whatnot. However, given that the Z only exists at rush hour, it would seem wrong not to include it.

Skip-stop service actually does not create a local-express relationship by the formal definition. If you have a sequence of stations that goes ZJZ, the Z would not be express relative to the J unless the J also stopped at both Z stops.