With the exception of service at Second Avenue, it was combined with the M train, which was rerouted from Lower Manhattan and South Brooklyn via the Chrystie Street Connection.

In Manhattan, the F and V made identical stops between 47th–50th Streets and the V train's Lower East Side–Second Avenue terminal station.

New York Times columnist Randy Kennedy wrote that four months after it opened, the service was operating at only 49% of capacity.

However, ridership had "increased 30 percent since it began, and every new V rider, as lonely as he or she might be, relieves crowding on the E."[9] The Straphangers Campaign and Queens Civic Congress organized protests in 2002 to request the V train be rerouted to the 63rd Street Tunnel.

[10] The overcrowding on the E train was, in part, due to riders' propensity to board an express even in situations where it offers no real advantage in travel time over the local.

Conductors were asked to make scripted announcements to urge riders to use the V, noting that they had a better chance of getting a seat on the train.

So the questions being asked privately, and sometimes very publicly, in Queens stations yesterday were: Do I take a train not going where I'm going and — God forbid — transfer?

[13]On January 23, 2005, a fire destroyed the signal room of Chambers Street on the IND Eighth Avenue Line.

[19] Additionally, this merger would open up new travel options for northern Brooklyn and Queens J/Z riders, in that it would allow direct and more convenient access to areas that were not served by those routes before such as Midtown Manhattan.