USB connectivity problems with Nexus 7 2013
Had similar problem with Google Nexus7 (2012).

To solve it I passed next steps:


Uninstalled incorrect Nexus USB drivers.
1) Previously, I installed windows default MTP driver to have ability to connect the device. It was a bad solution, because it made a problem for me to install new drivers.
Each time I tried to install latest_usb_driver_windows.zip from developer.android.com, Windows told me: 

“The best driver software for your device is already installed”

So I disconnected all USB devices, and in order to remove all previously installed USB drivers I used freeware tool DriveCleanup.
It was a bit unusual to run some tool, which perform some unknown system-related actions, but at the end of the day, it removed all USB-drive related stuff from Windows and didn't    harm a system.
In order to install proper USB drivers for my Nexus 7 on Windows 7 performed next:


Enabled debugging options on Nexus (Go to Settings > About tabled and tap 7 times on  "Build number" field);
Run "Settings -> Developer Options -> Revoke USB debugging authorizations", in order to start next negotiating between tablet and PC from scratch.
Enabled "Settings -> Developer Options -> USB debugging" to have ability to connect to the device by adb.
Connected device to PC. (Some informaition in the internet points, that in case of problems drivers installation, it's better to use USB 2.0, but I have only USB 3.0 on my PC)
Run "Device Manager" Windows tool. "Start -> Run -> mmc devmgmt.msc" or "Control Panel -> Device Manager"
Found Nexus Device, press right mouse button "Update Drivers -> Manual -> Browse", pointed to the latest usb drivers from google (In my case, they were downloaded by Android SDK manager: C:\Program Files (x86)\Android\android-sdk\extras\google\usb_driver). And press OK.
In most of cases, previous 6 steps should be enough to install drivers, but each time I received next error:  


"The folder you specified doesn't contain a compatible software driver for your device. If the folder contains a driver, make sure it is designed to work with Windows for x64-based systems."
So in order to make USB drivers fit my device, I performed next steps:


Run "Device Manager" Windows tool. "Start -> Run -> mmc devmgmt.msc" or "Control Panel -> Device Manager".
Found Nexus Device, press right mouse button "Properties -> Details" chose "Hardware IDs" from the dropdown, right mouse button on ID values "Select All -> Copy"
In my case it was:  


  USB\VID_18D1&amp;PID_4E42&amp;REV_9999&amp;MI_01&amp;MI_01
  USB\VID_18D1&amp;PID_4E42&amp;MI_01&amp;MI_01

Opened usb_driver\android_winusb.inf  file from latest usb driver directory by text editor, found [Google.NTamd64] section (there is also [Google.NTx86] section for 32 bit PCs). In amd64 section I found a ;Google Nexus 7 section. It looked like:  


  ;Google Nexus 7 %SingleBootLoaderInterface% = USB_Install,
  USB\VID_18D1&amp;PID_4E40 %CompositeAdbInterface%     = USB_Install,
  USB\VID_18D1&amp;PID_4E42&amp;MI_01 %CompositeAdbInterface%     = USB_Install,
  USB\VID_18D1&amp;PID_4E44&amp;MI_01

Basing on IDs, taken from my hardware:
USB\VID_18D1&amp;PID_4E42&amp;REV_9999&amp;MI_01&amp;MI_01
USB\VID_18D1&amp;PID_4E42&amp;MI_01&amp;MI_01
I added to the Nexus section next lines, using as last parameter of CompositeAdbInterface device ID with removed revision and all the text after it:


  %CompositeAdbInterface%     = USB_Install, USB\VID_18D1&amp;PID_4E42
  %CompositeAdbInterface%     = USB_Install, USB\VID_18D1&amp;PID_4E42&amp;MI_01&amp;MI_0

Nexus section of android_winusb.inf file started to appear next way:


  ;Google Nexus 7
  %SingleBootLoaderInterface% = USB_Install, USB\VID_18D1&amp;PID_4E40
  %CompositeAdbInterface%     = USB_Install, USB\VID_18D1&amp;PID_4E42
  %CompositeAdbInterface%     = USB_Install, USB\VID_18D1&amp;PID_4E42&amp;MI_01
  %CompositeAdbInterface%     = USB_Install, USB\VID_18D1&amp;PID_4E42&amp;MI_01&amp;MI_01
  %CompositeAdbInterface%     = USB_Install, USB\VID_18D1&amp;PID_4E44&amp;MI_01  


After this modification, Updating of USB Driver from Device Manager finished successfully. Maybe It is not the properest way to fix this problem, but it was first working solution, so I stopped further investigations.