This show is growing bigger than itself. The most important thing to me was addressing the issue of how much our old values and base instincts mattered in a society where technological advances continue to reduce the need to worry about, ironically, our basic needs.
While most people in modern society now accept that currently held ideas about society must change eventually, some do maintain that a core set of values continue to be valuable in the preservation of the well-being of society. For example, murder may be a more and more acceptable action in the future for various reasons, without the preservation of the values that recognize the sanctity of life. Euthanasia comes to mind.
The reality is that as society changes, our behaviours need to match the change to improve our livelihoods as a whole. While autopsies were largely forbidden by the church in the old days, it is considered neccessary today to discover preventive measures against diseases. Stem cell research comes to mind as people struggle with the idea of experimentation of what essentially constitutes unborn children.
This is where the real issues are addressed: we know some values must be held sacrosanct, while we must change our mentalities to fit the changing needs of our society, but where do we draw the line between values that can or cannot be changed? If you are on the preservation side you would be deemed too conservative, while those on the constant change side would be deemed hypocrites who change their values to suit themselves.
In line with our present hostility towards those who continue to uphold ancient values of fidelity and piety, Makishima is the conservative and villain of the show, who continues to believe that the freedom of man is sacred, despite the uncanny (and proven) ability of Sibyl to predict the violence of a person. Modern economics however does actually rely on the rule laid down by him: "value is only present in actions borne of the free will of a man", which is a simple transposition of what is said by Jonathan Reeves.
Finally the show continues to teach us that despite our disagreements and differences, we mysteriously still manage to live with each other (obviously with tension). Our opinions continue to be mere theory in practice, and that no matter the epoch, we can rely on our instincts to tell us when any member of our society has gone too far in attempting to enforce their beliefs on society as a whole.