VS2012 seems to remove the popup window for TFS check-ins that was in VS2010. It now seems to take over the team explorer tab in my sidebar, and buries the important things
For me, the best solution is based on iSid's answer: to add an external tool that pops up the old dialog. You can do this from Visual Studio: TOOLS -> External Tools… -> Add, with the following values:
Title: Checkin (or any name that should be displayed in the menu)
Command: C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\TF.exe (this is the default VS install location on Windows x64)
Arguments: checkin
Initial directory: $(SolutionDir)
Here is a screenshot:

You can invoke from TOOLS -> Checkin (or even assign a keyboard shortcut to Tools.ExternalCommand* as described here) and enjoy the old goodies with a new style:

Note that this won't work if a solution is not opened, because of the $(SolutionDir) variable. To workaround this, you can hard-code the path to your workspace instead.
Additionally, tf.exe can be invoked with 'shelve' argument, which will show the old-style shelving dialog.