I mean HYDRA infiltrated SHIELD in plane sight, right under his nose and GREW. Now we come to realize that SKRULLS have been on Earth longer than Fury knew and have been pulling strings JUST like HYDRA??!!
There was a moment in the Avengers Earth's Mightiest Heroes cartoon, that really showed Fury isn't as clever as he thinks he is.
During the Skrull invasion arc, Fury went into hiding along with his agent Mockingbird. But it eventually turns out Mockingbird was really a Skrull in disguise (not just any Skrull either, queen of the Skrulls), and that the real Mockingbird had been kidnapped.
I remember the queen saying something along the lines of "And to think...the great Nick Fury could be so easily deceived", after she revealed her form and disarmed him. The fact that she was right under Fury's nose the entire time and he didn't even suspect it until it was too late.
Whether it's live action, cartoons, or comics, Fury definitely seems like someone who thinks he's a lot smarter than he actually is.
Fury's ace-in-the-hole has always been Talos and his skrulls
Makes sense, and actually takes some guts to put out there. Everyone, including Stark, thinks Fury's a master spy. Turns out he may just be barely above-average without his shape-shifting allies.