So, something my friend brought up a little while ago, while he was binge-watching to get caught up (he missed most of Season 1, and hadn't watched any S2 until he caught up).
When the series started in Season 1, it was just after Iron Man 3. We knew what the "status quo" of the world was. Partway through the season we had Thor 2, and they dealt a bit with the clean-up, but nothing was really "shook up". Then, near the end of the season, we had Captain America 2, which really shook up the status quo, and they dealt with the fallout from that.
Between CA2 and now, however, our only look at the wider world of the MCU has been Guardians of the Galaxy, which had no present-day scenes on Earth. Which means that our only look at the state of the entire Earth has been post-CA2 Agents of SHIELD season 1, and all of season 2.
What my friend brought up, though, is pretty much "where is everyone?" While we understood the status quo of the world in most of season 1, it made sense that the heroes were off doing their own things. Stark was dealing with the aftermath of IM3. Thor was either off in Asgard (pre-Thor 2) or with Jane (post-Thor 2), etc. Now that things have been shaken up, and SHIELD are being treated like criminals (more so the end of S1 than in S2), and Coulson's team are fighting super-powered beings, where are all the heroes? Sure, they don't know Coulson's alive (other than Sif, who I've enjoyed seeing, I enjoy her as a character, and like her getting extra screen time), but they have to figure that someone is still running SHIELD, fighting against these people. Even if you argue that it's been primarily small-scale, after the prison break(s?) and the spectacle in Coulson's home town in this past episode, you'd think that someone would start digging to find out what was going on.
And while I have enjoyed season 2, I think that is its biggest flaw. In Season 1, we knew where the world stood, so it was fine to focus on a small group. But now that we have no clue what's going on in the rest of the world, focusing on the small group makes it feel like they're the only ones doing anything. Obviously, with the revelation at the end of this episode, it's going to lead us into some of this territory, but I feel his point (which, quite frankly, was made about 2-3 weeks ago, so before we knew this anyway) still stands. Agents of SHIELD works much better focusing on a small group when we understand what the status quo of the rest of the world is.