If someone sees malfeasance including lack of cooperation, intentional delays, bribes (corruption ring at large) during the case handling at a Swiss embassy, whom should be contacted, how can it impact the case of the person who files the complaint and will it have any positive outcome/impact to the workings of the embassy?

Based on my understanding, FDFA Head, Berkhalter, Didier is the person to write to. Is that correct or the embassy heads report to someone else?

Swiss consumer magazine article on reporting misdeeds

http://www.beobachter.ch/stichwortve...whistleblower/

Anything to add to this report:
http://www.tagesanzeiger.ch/schweiz/...story/22403378
?
I'm not sure if the original article at the sonntagszeitung.ch was available online at some point.
The Tagesanzeiger-arcticle links to the (heavily redacted...) internal reports, though.

If you have anything to add, you should call the EDA:
http://www.eda.admin.ch/eda/en/home/dfa/ref_contac.html

and request to speak to someone from the internal affairs department (interne Revision).
Be sure to be well prepared and able to proof your allegations because I'm sure they get a lot of calls from people who got their visa denied and thus try to take revenge on the poor soul who had to handle the request.
I'm not saying this is the case with you - just to show you what you should expect, should you call or contact them and to show you what they expect from you.

As you can see, the report is from November 2010 - it took more than a year before it was released to the public in December 2011.
So, whatever happens with you complaint - don't hold your breath for a change in the near future (or your remaining lifetime...)