Markjoy,
From what I've learned of this accident, I believe it is more an equipment issue, too.
Please, let me repeat CENIPA conclusions:
"7. There were no incorrect indications nor the appearance of unknown signals on the radar screens of the air traffic controllers’ consoles; this does not indicate, however, that there does not exist the possibility of improving the system, such as by the inclusion of audio alerts to indicate exceptional circumstances;"
Transponder fault was clearly seen in controllers screen (360Z360). The Z indicates that there is no information of actual altitute due to transponder failure, and the left or right (I'm not sure) 360 was the flght plan level.
...the way clearances are issued all over the world
Without clearance limt? Without route? Only "essencial informations" as controller said? What surprises me is that all Brazilians pilots and foreigners that operates here understands this is a clearance until Brasilia and then "as planed", and Legacy understood until destiny, as forsaw in ICAO regulations.