The main problem with "System 3" is that it have its own kind of "cognitive biases", like System 1, but those new cognitive biases are designed by marketing, politics, culture and whatever censor or makes visible the original training. Even if the process, the processing and whatever else around was perfect (that is not, i.e. hallucinations)

But, we still have the System 1, and survived and reached this stage because of it, because even a bad guess is better than the slowness of doing things right. It have its problems, but sometimes you must reach a compromise.