Q: Do you feel there are any advantages with the new Extakta 66 over the old Pentacon Six?

A: The Exakta 66 has a much more modern design and appearance, which may or may not be relevant to you.

The Exakta 66 has a better advance lever than the Pentacon Six (even in Mk I version, but better still from Mk II). 

It also has (from Mk II on) a spring lock on the back to prevent accidental opening.  (But if you use the Pentacon Six in its case, this will never be a problem.)

It has a switchable pressure plate for 120 and 220 film (which was not considered necessary on the Pentacon Six).

It is likely to be a lot newer than most Pentacon Six TL cameras (made 1968-1990). 
Exakta 66 (Mk I) was made from about 1984 to about 1990, Mk II from about 1991, Mk III from about 1996 to 2000.

I have heard reports that the film advance mechanism in the Exakta 66 is better than in the Pentacon Six, but I do not know if this is true.  In any case, if you load the film correctly, this will not be a problem, unless the camera is faulty.

You might get an excellent export-quality Pentacon Six or a doubtful quality Pentacon Six made for the East German market. It is impossible to know.  (However, even in communist times, the East Germans were proud of the quality of the cameras they produced, which were (in my opinion) way better than anything produced at the time in the USSR.)
All Exakta 66 cameras were made in West Germany (from 1991 the new, unified Germany) to the best world standards.

The Exakta 66 metering prism is linked to both the shutter speed on the body and the lens aperture (on Joseph Schneider lenses only), providing fast full-aperture metering – though the stop-down method that I use on the Pentacon Six with its TTL prism is almost as fast.
However, bear in mind that the metering only works with the Schneider lenses, which are hard to find and generally expensive – although they have the advantage (with the exception of the standard lens) of being smaller and lighter-weight than the Carl Zeiss Jena lenses.  For instance:

• the 60mm Schneider Curtagon is much smaller than the 50mm Carl Zeiss Jena Flektogon – but it’s not as wide an angle
• the 150mm Schneider Tele-Xenar is much smaller than the 180mm Carl Zeiss Jena Sonnar – but it’s a shorter focal length, and not as large an aperture

You could consider the Exakta 66, the ultimate “upgrade” to the Pentacon Six, made in West Germany by Schneider using the chassis and some parts of the Pentacon Six. 
The Mk III version is the best of the three versions, with a built-in mirror pre-release.  Pentacon in Dresden still service these – and Pentacon Sixes! – , and a few years ago they upgraded my Mk I Exakta 66 to full Mk III specification.

I am very pleased to have both cameras, and do in practice use the Pentacon Six more than the Exakta 66!  Why?  It cost less, is easier to replace, and is protected by its case if given a bit of rough handling.