One opinion, and there will be plenty of those, is that the recruiter looked at your transcripts and GPA and decided that they need to see how you will perform on the basic principles put forth on the NFQT.
Everyone has an excuse for why they performed poorly in high school/college. The Navy doesn't care. Period. What the Navy sees is that your transcript shows a documented below average performance. The reason is irrelevant as far as the Navy is concerned.
Your statement about homework being arbitrary does make me pause. The Navy Nuclear Power Program is built around compliance with procedures and following orders, back by maintaining a healthy questioning attitude. I realize those may seem to be contradictory to each other. The key is to find the balance. The Navy has a set approach to teaching subjects in “A” School and Power School. Comply with this methodology, do the homework because they tell you to and it provides practice in said methods and the road to success is much less bumpy.
The questioning attitude comes in to play when something seems strange or you really do not understand something. Call it a “gut feeling” or whatever. As you gain experience, you will come across situations where the hair stands up on the back of your neck or you get this feeling that something just isn’t right. At that point, question what you are doing and why.
One last bit of advice. Stop trying to figure out “Why?” and simply focus on doing your best. The more effort you put into the program, along with your attitude, almost always yields better results. I scored a 99 on the ASVAB and a 65 on the NFQT in 1990. I graduated 4th in “A” School, top 10% in Power School, first qualified at Prototype, made 1st Class in 5 years, Chief in 8 and retired this past December at 20 years. Effort and attitude were 90% of that success. If you want it and are willing to put in the effort, the only thing holding you back will be yourself.
Good luck and keep us posted.