The big one seems to be that pythran is targeting only a subset of python with the goal of getting faster performance, while Nuitka is aims at being able to compile all valid python programs (currently only up to python 3.4), but in doing so it has fewer opportunities for optimization and thus gives you slower performance than pythran. Pythran also introduces its own type annotation system you have to use if you want to get good performance.

So If you write a python program that is compatible with pythran, then pythran will almost certainly be much faster than nuitka. If however you take a random python program it will almost certainly compile with Nuitka and almost certainly not compile with pythran.