I love m F4S. I've used it almost exclusively with AI'd MF lenses, so I really don't know how AF performs with it. The 105/2.5 is perfect on it for me. And I can walk around with a 50/1.4 in my jacket pocket. The viewfinder is awesome.
I've never used a F3, so don't know how it compares.
My only concern with the F4S it is the size and weight. I know I can slim it down by removing the battery pack, but it just fits my hand with it on. Size and weight is not too bad, but I'm now doing more travel and just enjoy city wandering. My favourite digital is my xPro-1, and I'm moving to a Leica M body for film. The size and easy x mount adapting of the Leica lenses to Fuji seem to make more sense at this point in my life. It's more about how the two systems will work together and the size.
I've thought about selling the F4S and Nikon glass - it's all in beautiful condition - but at the price the bodies go for today, I know I'll end up regretting it. At times I just gravitate back to the F4. It makes me smile. You can buy a mint one for very little money today, which just makes it a fantastic choice if you want to try it.