So, no giant robots during this W.W.II

Smart choice.

instead, this fic would focus on the trials and tribulations of the people

in a secret

japanese bunker complex (demeaningly referred to as Tokyo-3,)

and whoever picks this up can make allusions to their sister complex
Tokyo-2.

In actuality, Rei is the first partial success of Tokyo-3's true mission:

The creation of a 'Master >Race' to replace us imperfect humans.

I suppose the Germans would prefer the Aryan look but that might not have
sat well with their Japanese counterparts...

Just an Idea on my head at the moment, I am quite willing to donate it if

it catches somebody's >imagination.

This idea reminds me of a fic some time ago that had the Ranma cast starring
as the crew of a WW2 sub under Happosai.
Should be worth it. I hope someone picks this up.