Agreed. As much as I love this game, making us play as a the worst character possible is not something I enjoy. I get what the dev is trying to do by this, but on the other hand I feel like it takes away a bit of the mystery from us players, and how we know something the MC doesn't.
The other organization characters aren't exactly noteworthy for me either, and not once was I intrigued and wanted to know more about them. Zena is the only one I actually care about, and even that is just cause Eris fixed her up a bit, and it's actually something that MC is doing instead of the bitch Nyx.
Now that I'm thinking about it, I know it would have been harder to do, but (just my opinion) now that Zena is our (wo)man on the inside, we could have experienced the Org part of the plot from her POV instead. (Though that wouldn't really change the real problem I have with it).
But I'm guessing it's all to setup Jasmine/Lethe and potentially Nyx somehow becoming a vessel for Lethe or something, so we get some more depth into the characters, but it all falls apart because of the org agents being as dislikable as they can be, and not just cause they are THE ENEMY, but just because they are.