Hi,
I have to say there are a few misconceptions out there.
1. The S5 pro not only has an AA filter! It has - according to a technician who examined it - the strongest ever built into a DSLR. Except for the few samples that had it removed. A german guy (nickname "nightshot") has been removing AA filters of different DSLRs for many years. When he was asked to do this with an S5pro (by a friend of mine) he worked a long time for a solution and the first thing he wrote was that the AA filter in the S5pro is really thick! He then had to look for an IR filter that had the right strength in order to not disturb metering of the WB and the AF which he said was very tricky. I closely inspected the results from the few (less than 5) S5pro cameras he converted and found that the additional artefacts in the AA- less version were too strong to accept in return for the slightly higher acuity or sharpness. I passed on the experiment and left my S5pro untouched (I still have it).
2. Fuji did not add the 12MP as an option to impress the customers with a higher number. Unlike normal Bayer Pattern sensors the pixel array in the Super CCD as used in the S2, S3 and S5pro does not have pixels in straight geometric lines, but a more or less complicated pattern (S2 pro 6 million physical pixels, S3 and S5 6 + 6 MP) or interleaved lines. Epson used this technique in their flatbed scanners to improve resolution without actually implementing CCDs with the indicated physical resolution (like 1200ppi etc).
So: The native files size of any S2 - S5pro is 12MP really, 6MP JPEGs are down- interpolated from that. The real resolution of course - as with the Epson scanner - is not 12MP, but - depending on the model - slightly above the single resolution of 6MP. S2 pro with a very sharp lens had a quite crisp 12MP output, the S3pro added the best DR of any DSLR for many years to come , it's AA filter was weaker than the one in the S5pro.
What one has to keep in mind is the insane amount of interpolation going on in an S3 and S5pro:
1.) 6 --> 12MP up- interpolation because of complicated pixel array.
2.) Interpolate S and R type pixels in order to increase DR.
3.) Bayer pattern interpolation.
No wonder there are artefacts. ALmost a wonder that those cameras put any photos out at all. And beautiful ones!
I have to say that despite the lack of biting sharpness the files of the S2 (my first DSLR in 2003), the S3 and S5 have something in their look that is just so... natural. The dramatically larger DR - specially in the lights and extreme highlights (where it really counts) also contributes to this, I have never seen files so malleable, so consistantly good- looking even with the most modest lenses. Even with a Nikon kit zoom (18-55mm VR plastic phantastic) the S5pro produced wonderfully looking files. I took the S2/S3/S5 twice to India and made many thousand files with it.
As for the best RAW converter for the S2-S5: That is an easy one: Fuji Hyper utilities, it produces the smoothest files with the best (by far) colours and WB. Lightroom gets contrast curves, WB and tonality/ colours ok, but not nearly as good as Hyper Utilities. Workflow is frustratingly slow, but the resluts are just better than the rest.
Compared to the old S3/S5, the X-E1 and X-Pro 1 with the "X-Trans" has of course much better detail and better high ISO; but colour, tonality and DR are clearly inferior to the old DSLRs.
Cheers
Bernie