One of the core things about SHIELD in the comics was its role as a continuity piece in the Marvel Universe. Partially to promote its own feature, and partially as a tool for binding Marvel's superhero comics together, SHIELD often appeared as the backdrop in multiple Marvel titles.
Need the CIA for a comics story? Use SHIELD.
Need some official monster hunters (for anybody but The Hulk)? Use SHIELD.
Need a non-superhero-level-but-capable supporting bodyguard/thug? Make them an ex-SHIELD agent.
Need a gang of disposable, but high tech punching bags? Use SHIELD's enemies HYDRA or AIM.
The TV show, however, has drifted far, far away from this. Ever since The Afterlife story arc, the show has removed itself from the MCU, almost splintering off into a world of its own. Even mention of Daisy and Yo-Yo as being Inhumans has gone by the wayside (of course, given how The Inhumans turned out, perhaps the less said the better).
I don't claim this is bad, but in many ways, the show isn't The Agents of SHIELD anymore beyond the name.
So, if it isn't AoS anymore, is there anything in comics or other media that it resembles more closely?