Very good question. I will need to do some homework to list all of them. One change is that the ratchet wheels are now under the bridge. You can see that in the photo below between a ruthenium coated brass movement and the more recent gold....
This is one of my favorite FPJ.Only hesitation I have is my perceived difficulty of the winding position.I suppose it's a matter of adjustment and getting the hang of it.
There haven't been any modifications to the movement. The change of the ratchet wheels I highlighted was only a design change and didn't impact the movement.