and these arguments never seem to consider the issue of manpower.
making a line longer, means you need more people to run it.
let's take an example of all the claims the J or at least the Z, should go via the Montague tube.
The J/Z operates on what we can call a "single base" model. with the exception of the crews that report to East New York Yard and one crew whose day ends at Broad Street, everyone starts and ends their day at Parsons/Archer. this is because the J's length makes it tolerable. a full round trip, including relaying the train at broad street, is just about two hours, with the possibility of a quick "comfort" (read; bathroom break) at Broad if we need it, and two hours is about the limit of our average physical tolerance to continus work.
Now, most J jobs are three round trips and most fit into a standard 8 hour working day. you start making the line longer, You will ether start having to dig into more jobs with built in automatic overtime OR, cut it down to two trips, meaning you need MORE crews to keep service levels the same.