For example, in the German legal system there is a clear delimitation of responsibilities: the people at the "pointy end" of the Lathen Maglev accident are being prosecuted, whereas the managers who decided against incorporating service vehicles into the technical protection system are not being prosecuted. But whichever way it goes, someone is still being prosecuted.
Maybe the people at the "pointy end" really didn't do what they had to independently of the management having refused to incorporate service vehicles into the technical protection system.
I believe that in German Law the managers you mentioned COULD have been prosecuted if their conduct clearly showed an injustified disregard for safety. We should ask the german prosecutors why they weren't.
Not all prosecutions are unfair or irresponsible. My point was that prosecutions tend to be broader and many times exaggerated if there isn't a clear delimitation of responsabilities by a given industry.
As for the examples of regulation and clear delimitation of responsabilities, they were just given to show what this clear delimitation of responsabilities would be.
Asking the pilot to ask for a standardized IFR clearance, for instance, just means that he should know whether or not he should try to contact ATC to ask permission to change his FL if he doesn´t get the expected clearance to change FL a considerable time after he enters another airway in which he is expected to change said FL.
Asking the pilot to follow his fight plan and to know what are the FLs he was supposed to fly in each airway would help to prevent accidents. If he is not contacted by ATC, he should at least ask for confirmation of his (supposedly wrong) FL from ATC.
You might say that it could represent an overburden to controllers (answering requests from pilots in such circumstances) but it also could work in the opposite direction as pilots (or crews) would act as a backup to ATC. And increase the likelihood of net being killed themselves
Anyway, the main point is:
If (IF !!) those were the rules, and they weren´t followed, then we have a prosecution. If all the regulations were followed, however, no matter the conduct of pilots or controllers we won´t have a criminal lawsuit.
(P.S.: I am refering to future rules on this matter, not specifically to the GOL/Embraer collision)