Ion conductivity of Nafion is the important feature in comparison to PTFE. Nafion is used as an ionomer in fuel cells. It is also utilized for RDE/RRDE experiments as binder to electrodes.
In the case of Fuel cells, the Nafion ionomer is added to impart the ionic conductivity. In some applications like preparation of supercapacitor electrodes, the PTFE / PVDF is used. In this case, the function is just to bind the particles together. So the function and the application is very important while choosing the materials.
Nafion has hydrophilic channels bristling with sulfonates that wll allow water and some ions all the way to your electrode surface. The PTFE ought to be hydrophobic and essentially waterproof.