One way you can solve the fading problem is by having Yoda and Ben die in the Clone Wars and their physical bodies in the OT are created by the Force to maintain it's balance.

All that business in the PT about the chosen one then makes sense.

When Anakin is born the Jedi greatly outnumber the Sith. By the time he turns there are only two.

We could see them both 'defeated' too but mysteriously return back to physical life.

Even though they are defeated they can't fully pass away while there are two Dark Side warriors ruling the galaxy and Anakin/Vader is the mystical mechanism preventing both sides from gaining the upper hand.

Palpatine can't train armies of Sith while Vader lives and he can't kill Vader while the last Jedi remain hidden.

Ben takes on Luke as a pupil so Vader can now physically defeat him but as Luke is untrained his spirit lingers to keep the balance the Force needs.

The Anakin persona in Vader begins to reawaken after meeting his son so Yoda's body begins to fail.

When Palpatine is dead Luke is the last Jedi so Anakin can linger in spirit even though his machine maintained body has died.

The only way you can explain this is subtly and visually in a PT re-jig.

That way the PT would actually enhance aspects of the OT without having to change it (which is how it should always have been).