I understand the desire to believe that there's a much larger scheme at work with what we have so far but I don't think there's any substantial or compelling evidence to believe the mind gem was in Loki's staff. I feel much the same way about the theory that Loki deliberately allowed himself to be imprisoned in order to be close to the Gauntlet. If the gem in the staff is the mind gem, then it has suffered from the type of retooling that is usually bemoaned around these parts. There are three separate instances in the film where they make it clear the staff's power comes from the cube: Cap mentions it handling like a HYDRA weapon, Fury explicitly stating it's powered by the cube and Banner saying its energy readings are consistent with the cube's own.
It seems to me that the theory only really holds water if you assume the film is actively feeding you misinformation, which seems highly unlikely. I don't think Whedon would go to such lengths to establish the origins of the staff's power if it was part of a bigger story in the future with a completely different mythology.
It seems to me that the theory only really holds water if you assume the film is actively feeding you misinformation, which seems highly unlikely. I don't think Whedon would go to such lengths to establish the origins of the staff's power if it was part of a bigger story in the future with a completely different mythology.