What do you mean with "automatically process RAW photographs"?
Software cannot "automatically edit" photos easily because it does not know what you wan to see and show.
Software can only "auto-optimize" photos based on certain preset parameters which what I suspect you are after. However the results are very varied and not something that can really be considered reliable "automatic editing" of photographs.
Now there is another aspect - camera profiles:
If you use a product such as Lightroom or the manufacturer's own product (Digital Photo Professional for Canon, no idea about Nikon) it will apply a camera profile to interpret the RAW data to produce an image that will look similar to the preview in the camera.
A last option that is impractical outside of a clearly defined environment is to always include a known parameter (e.g. a grey card) in the same spot of a photo.
You should then be able to use something like a Photoshop action (or maybe you need to write your own plugin) to "edit" or "optimize" the photo relative to that known parameter.
However unless you are a studio photographer or monitor some experimental setup this is unlikely to be a practical approach.
I hope I haven't misunderstood your question.
Just a little pointer - if you are shooting in manual mode and don't like the results, maybe you should try a semi-automatic mode? Maybe even post some examples so we clearly understand what your problem is.