There is very little training value to be gained for those going to submarines as well. It's not like current submarines have a WWII era destroyer engineroom attached to a piece of a submarine hull, complete with an S7G core that originally didn't use control rods. There are only two logical conclusions I can draw why prototype still exists:
1) The systems that are similar between prototype and submarines allow junior Sailors to qualify more quickly, since there wouldn't be enough manpower on board to completely train a guy who hasn't seen the inside of an engine room.
2) It works, and has been working for over 50 years, so why fix what isn't broken? No one wants to be 'that guy' who changed the training pipeline and then had the Navy's first reactor accident.
I lean much more heavily to 2 rather than 1.
The idea, 20 or so years ago was that
1. NNPS was an academic/mental filter, i.e. to filter out those who do not have the ability to absorb and regurgitate the theoretical and knowledge based parts of being a nuke.
2. NPTU was a hands on/physical aptitude filter, i.e. to filter out those who just had no aptitude for operating and controlling the actual ships systems.
So, my theory, about 10-15 years ago the Navy started having a
real hard time filling nuclear billets because the civilian sector had a lot of jobs, people could afford to go to college, and things in this country economically were just peachy. So, the Navy removed the filter elements and NNPS and NPTU became pumps. Fast forward to 2010. Suddenly, lots of people want in the Navy (steady, stable employment, no layoffs, good benefits). Lots of
High Quality Applicants are knocking on the door. I think that very soon the filter elements will be re-installed, and the NPTU's will go back to doing what they are supposed to do.
Oh yeah, and also your #2, ain't no one wants to be
That Guy 
Have A Day

-Matt