Damn this thread keeps exploding. Hard to keep up, but in a good way.
Thanks for your input guys. I think I'll go with "inherit design flaw", although it doesnt quite click with me.
A central idea in Blade Runner and many sci-fi stories is that complexity makes control impossible. The more sophisticated something gets, the harder it becomes to predict. Given time, emergent properties inevitably arise faster than the creator can account for. Yes, Wallace seemed to have found a way to ensure compliance in his new models, but its only guaranteed in very specific situations. He knows that given enough time out in the world, replicants will start developing their own emotional responses to stimuli. Hence the baseline test to catch and quash any glitches. But given the numbers of replicants secretly lurking in the shadows looking for their chance to rebel, its not working very well.
As far as the whole point of replicant disobedience, you have to remember that they're biological... physically human, not machine. You can't just install programming like a computer, or even flip a switch in a gene to make them docile and obedient (don't listen to Attack of the Clones). The only way you'd be able to do something like that is through brainwashing. Probably subliminal into whatever they use to educate them, or implant the memories into them. But like any brainwashing, it can be overcome by the individual at any time if they have the right motivation. They knew this was a possibility, hence the baseline testing.
I would contend that the biological vs. mechanical distinction is irrelevant and that is one of the messages contained within the film. Joi is the ultimate refutation within the BR universe, a complex piece of software potentially on the verge of exhibiting the same emergent behaviours as replicants (hence all the debate we are having in this thread alone), and the possible precursor to another artificial revolution that grows beyond the intent of its creator, given enough time and experience.
Of course, this all reminds me of an episode of Star Trek: The Next Generation.
The Measure of a Man. Lt. Commander Data, an android, is on trial to determine whether he is the property of Starfleet or a sentient being deserving of the protections granted by the Federation. Riker, Datas colleague and friend, is forced by the presiding JAG to serve as the prosecutor against Data; if he doesnt do it well, the case is forfeit and Data gets broken down to parts. In the courtroom, Riker argues that Data is nothing more than a machine, demonstrating the fact by removing his friends arm and shutting him down via a secret switch before delivering a devastating line:
"Pinocchio is broken; its strings have been cut."
Picard, who is in charge of Datas defense, is despondent after a recess. He uses Guinan as a sounding board and their resulting conversation is one of the best scenes in Trek history, and one that could be lifted straight out of Blade Runner:
https://www.youtube.com/watch?v=6Eg67jDh2Ts
Back in the courtroom, Picard refutes Rikers argument that Data is a machine by stating it doesnt matter:
"Commander Riker has dramatically demonstrated to this court that Lieutenant Commander Data is a machine. Do we deny that? No, because it is not relevant: we, too, are machines, just machines of a different type. Commander Riker has also reminded us that Lieutenant Commander Data was created by a man; do we deny that? No. Again, it is not relevant. Children are created from the 'building blocks' of their parents' DNA. Are they property?"
Picard goes on to showcase Data as being more than the sum of his parts by examining the significance of his personal belongings, which serve no functional purpose but mean a great deal to Data. Picard asks why Data has a holographic portrait of the late crewmember Tasha Yar and no one else. Data, uncomfortable, confesses that they had once been intimate.
Ultimately, the JAG rules in favour of Data, with her speech speaking to the core ideas Blade Runner tasks us to ponder:
"It sits there looking at me, and I don't know what it is. This case has dealt with metaphysics, with questions best left to saints and philosophers. I am neither competent, nor qualified, to answer those. I've got to make a ruling to try to speak to the future. Is Data a machine? Yes. Is he the property of Starfleet? No. We've all been dancing around the basic issue: does Data have a soul? I don't know that he has. I don't know that I have! But I have got to give him the freedom to explore that question himself. It is the ruling of this court that Lieutenant Commander Data has the freedom to choose."
Trek being Trek, the episode provides us with an optimistic portrayal of how we can expand our sphere of consideration beyond ourselves. Blade Runner being Blade Runner, it gives us a fleshed out nightmare where these questions are not even debated, and humanity has walled itself off from anything other with tools of violence and subjugation.