The gateway tunnel has been postponed indefinitely. But no worries, apparently the only reason the Gateway Tunnel was necessary was because the MTA previously refused to run things efficiently.

http://transportationnation.org/2012/06/14/ny-mta-chief-says...

Also interesting: "The Regional Plan Association, which held the conference at which Lhota spoke, and other advocacy groups have expressed support for through-running—at least until Gateway Tunnel gets built."

I.e., they want to be more efficient, but only as a stopgap measure until the tunnel is built.

(Also check out Market Urbanism's blog post on the topic: http://webcache.googleusercontent.com/search?q=cache:ycccmpt... )