A patch in newer kernel (3.19 and later) has a fix for this as below:

commit 2484f40780b97df1b5eb09e78ce4efaa78b21875
Author: Dan McLeran <daniel.mcle...@intel.com>
Date:   Tue Jul 1 09:33:32 2014 -0600

    NVMe: Add shutdown timeout as module parameter.
    
    The current implementation hard-codes the shutdown timeout to 2 seconds.
    Some devices take longer than this to complete a normal shutdown.
    Changing the shutdown timeout to a module parameter with a default
    timeout of 5 seconds.
    
    Signed-off-by: Dan McLeran <daniel.mcle...@intel.com>
    Signed-off-by: Matthew Wilcox <matthew.r.wil...@intel.com>
    Signed-off-by: Jens Axboe <ax...@fb.com>


However, this patch is not included in 3.13 or 3.16

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https://bugs.launchpad.net/bugs/1465136

Title:
  NVMe shutdown and suspend delay time is too short

Status in linux package in Ubuntu:
  In Progress

Bug description:
  A hardware vendor reported that NVMe didn't implement power management
  correctly during shutdown/restart and suspend/resume as below:

  =================================
  However, when it comes to shutdown/restart, the Power Management Events (PME) 
are not correctly implemented.

  When the host (Linux/Driver) sends the PME_TURN_OFF message it should
  wait for PME_TO_ACK from the device.

  Microsoft Windows versions typically wait for 5 seconds.

  The Linux OSes doesn't wait for the PME_TO_ACK from the device and
  simply turns off the system instantly immediately after the
  shutdown/restart.

  This is not the way to treat PCIe storage devices. The host should allow the 
device to properly shutdown.  Otherwise the disk will go in to rebuild during 
next power on which takes a while resulting in OS finding the device not 
responding and disabling it and not loading the driver for it.
  =================================

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