Really, though, I wouldn't have a problem with the existence of spectres if there were more people in the games going "hey don't you think that this whole organization that can do whatever it wants without accountability is kinda messed up?" Like they don't explore the concept at all really it's just an excuse to give Shepard, and by extension, the player, more agency.

You're telling me that the game series where you become a member of the spectres which is basically the Space CIA who have the ability to act with total impunity under the law and is portrayed purely positively might have some problematic elements?