I think the idea behind Nuitka is to compile Python into an executable, rather than interpret a script using a fully generic interpreter, but without (or with minimal) limitations, falling back to libpython's implementation if necessary.

> In the future Nuitka will be able to use type inferencing based on whole program analysis. It will apply that information in order to perform as many calculations as possible in C, using C native types, without accessing libpython.

I believe the difference with PyPy is that PyPy tries to do this using just-in-time compilation and nuitka uses ahead-of-time compilation.