As far as physics being ahead of the other sciences, it may be because physics has adapted to the quantum nature of reality faster than biology and chemistry. The reasons acupuncture has taken so long to be accepted is that biology is still based on a Newtonian model and cannot accommodate notions of chi and meridians.
Ultimately, physics can only predict where a particle might be. It can never know for sure.
As for the "success" of the softer sciences: I know that one can successful fight poverty, do HIV prevention, reduce truancy, etc. If the country would spend as much money and focus as much manpower/brainpower as they did on the Manhattan Project, then there would be success. Lack of "success" in the "soft" sciences, is often attributable either a) to a lack of investment to demonstrate the success; or b) adoption of standards of proof which eliminate the ability to demonstrate success.
With regard to philosphical naturalism, I found this brief essay on the web:
http://dwardmac.pitzer.edu/Anarchist_Archives/bookchin/philosonatural.html
Finally, as for complexity, I have always like this quote from Bergson: ""There is nothing in philosophy which could not be said in everyday language."
Brian Dauth Queer Buddhist Resister