I think you may be focusing too much on supervillain than superspy. From what I'm getting out of both him and Skye, he was a sleeper agent for long enough to be trusted in SHIELD. I am missing vital information, like what made his position and how things went down after, but just due to the nature of the game, I'm thinking we should be prepared for something more subtle.
But if the tracker's the best we can manage, we'll have to work with that.
PRIVATE.
But if the tracker's the best we can manage, we'll have to work with that.