The main differences here is in the options screen you can define how wide the pixels are on screen in relation to your chosen resolution, where as before it was some weird scaling algorithm and you had to tell the app what your aspect ratio was. That's not a thing anymore, it automatically determines your aspect ratio so all your pixels come out nice and square. You can still adjust the bit depth with a handy little slider in the Retro FX config screen. The biggest addition to the Retro FX Shader is dithering. This adds a tremendous amount of smoothness to the whole look, especially if you set the bit depth really low (ramp up that dither spread!) I've even given you the option of choosing what type of dither effect you prefer, ordered, or random. Just assign whichever PK3 suits your tastes!
Screenshots:
Spoiler:Imgur Album
And download:
Mediafire