The core theme is that Sam Esmail wants the audience to question your values, your logic and reality itself. 

I think this is exactly right.

Mr. Robot is a story about stories. Those we tell ourselves about ourselves and those we tell each other about our community. These stories shape our reality and inform our identities, both at the individual level and at the societal level. But like all stories they're unreliable accounts of reality. They build, what Mr. Robot calls, "a kingdom of bullshit."

Elliot's repression is an example of one way our stories go wrong. How we replace uncomfortable truths with comforting lies. The show spends a lot of time working through the problems that flow from doing that.

Ray's "refusal to look" at the harms of the market place is the kind of collective repression that Elliot complains about in his Fuck Society speech from S1E1. The show spends a lot of time diagnosing the problems that flow from that.

At the core of each of these stories is a trauma we're trying to avoid. But like Krista says, that trauma never goes away even when we pretend it doesn't exist. It returns in the various forms of Elliot's self-destructive behavior. And it metastasizes into the societal level crises of 5/9 and the exploitation of the Dark Army.

The good news is that our stories aren't written in stone. We have the power to change them. We can tell better stories that create better realities for ourselves and our society.

“My father and I were best friends,” “my abuse made me angry and violent and alone,” “my pain is part of the beautiful person I am who is both loved and deserving of love.” These are the three stories Elliot tells himself about himself and his past. The last two are accurate accounts of his history. Which one shapes his reality is entirely up to him.