The only advantage we can see to pocket/retrofit windows would be that it is a quick and easy installation.  But does this benefit the homeowner or the contractor?   

A pocket/retrofit window can be installed quickly, however there are many disadvantages to these types of windows.  First and foremost, since the new window is installed on top of the existing frame, you end up with a smaller window that has a large frame area and a less visible glass area.  The homeowners old casings remain around the window, and the exterior is not re caulked which could lead to leaks.  Also, there is no way to re insulate a pocket/retrofit window because there is not enough free space between the old frame and the new one.  This results in a lower energy performance of the new window.  The end result is a window with a large frame, less visible glass area and large flashing around the exterior giving a cheap and unprofessional look.

There are major benefits to using a new construction type window with a full frame installation.  When the existing window and frame are completley removed you have knowledge of the state of your walls and insulation around the windows.  Many times rotting wood is found and replaced at this time and the entire opening is re insulated.  This way if there has ever been a leak it will have been seen and remedied.  Also, the new window is the original size, not several inches smaller on all sides.  You will never loose visible glass area.  The new windows are caulked and sealed on the exterior providing the homeowner with a truely energy efficient new window.  

Since we pride ourselves with the quality of our workmanship, we prefer new contruction windows with a full frame installation.  We only do pocket/retrofit windows when there is no other way to do the installation.

Please beware of the cheap and very inexpensive window prices that are commonly advertised.  Installation is a major factor in the quality of your new windows.