A lot of your points are solved with attrs. I suggest reading up on it if you haven't already. http://www.attrs.org/en/stable/

I think organizing / refactoring a bunch of named tuples would be a mess. In one code base I maintain I switched a bunch of namedtuples to attrs classes and the code instantly became more readable / maintainable.

The downside to the namedtuple is that it's a tuple and can be unpacked as one.

for x, y in points: print x, y

# vs.

for p in points: print p.x, p.y

# ... now go and add a z to the point class and see what happens to your code.