All of this is a big part of why the show is struggling to find its sea legs right now. Marvel is asking us to understand that SHIELD is a complicated, compromised organization that on balance does way more good than bad. In that way, it is an analog for our own real life military/paramilitary/espionage organizations. At least, we HOPE so. So it's good that they have a whistleblower/hacker character like Skye - who is there to question things that the trained agents don't, but that we (civilians) WOULD. The tension is natural, and obviously it was a big part of the B-plot in The Avengers, too. None of them trust SHIELD - but they're not like, "Death to SHIELD!" either. It has its place, as the movie demonstrates.
The show, on the other hand, is not able to drive that home as successfully because the big revelations about SHIELD (how it's run; who runs it; who has oversight - if anyone; whether they really have our best interests at heart; who/what are they protecting people from?, etc) are all reserved for Cap 2.
Next season, they'll be tasked with leading up to Avengers 2, and will be hamstrung in the same way vis-a-vis plot points reserved for that movie, but at least we'll have a better idea how we're supposed to feel when SHIELD wins one on the show. Or loses one. And where the Bus and its crew fit in. Right now, we have no idea about any of that.
Edited by BklnScott, 15 November 2013 - 06:25 PM.