To be fair, this version of SHIELD hasn't really dealt with supernatural beings, as you can see, they are still discovering and are shocked and surprised about superhumans (mutants) existing. I mean the Avengers still consist of humans with powered suit and serum enhanced, gods and aliens.
For this group, outside of Coulson, this is their first experience with humans with human born powers, they made that very clear. Plus you also have to remember, these guys are on the lower pay grade and there are the higher ranked ones like Nick Fury, Maria Hill, Hawkeye, etc... These guys outside of Coulson (maybe?) are simply out of that league.
You also got to keep in mind that the events in this show is an aftermath to the Avengers, where Fury specifically stated that they did not know there were forms of higher beings before the events of the Thor film so yeah these small group isn't exactly trained for these kind of stuff, hell in the Avengers Black Widow and Hawkeye talked about not being trained to deal with Thor and Loki and those two are SHIELDs top agents.
I still think this show could be much, much better but it doesn't need to be dark, just better writing that believes their audience is smarter than they think they are.
Also, despite declining ratings, it seems that their target audience (18-40 viewers iirc) stayed consistent and that is why it got approved for a full season. The shoes really needs to just pick up audience int he last few episodes and it'll be renewed for a second season, especially if they really tie it all in with the films.