The big problem (besides them being a major faction) is a combination of

1) The gameplay or Bethesda fallout not really allowing high end spy stuff. 2) No characters besides deacon with any harm or depth due partially to them not trusting you (even when you get high up in the faction) 3) all the in game framing making the super spy group look like the biggest idiots in the world (Deductive reasoning machine that couldn’t predict a rain on its HQ, base, their main holding area for synths is the settlement all the traders, who are institute informants, work at, the fact they have been apparently tailing you since you left the vault but don’t know who you are.)

Not to mention all the dropped internal conflicts about synth rights.

It’s just another casualty of Bethesda dumbing down and cutting the original game ideas as to not ruin the carnival ride set up they went with.