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Dmytry comments on Neurological reality of human thought and decision making; implications for rationalism. - Less Wrong
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The first thing that should be noted is that any theory of a massively parallel system simply must be abstracted in order for humans to be able to understand it. Take, for example, anything that tries to describe the behavior of a large population of people: economics, sociology, political science, etc. We always create high-level abstract concepts (describing the behavior of groups of people rather than the fine details of every single individual).
Keeping that in mind, psychology is intentionally high-level and uses abstract concepts, which have an as-of-yet unclear correspondence to the lower level descriptions of the brain we have from neuroscience. This relation is analogous to that between high-level descriptions of large populations, and actions of individuals.
The answer then, in my opinion, is to keep working towards bridging the gap between the lowest level which we have a near-deterministic understanding of (we know how individual neurons work and a little about how they are connected in the brain), and the higher level intuitive descriptions of mind which are descriptive but not predictive. The massive parallelism required by the low level theories is NOT ignored, so far as I know, by neuroscientists and neuropsychologists, which makes me a bit confused as to why you think further emphasizing the role of parallelism is necessary.
Unless of course, you are criticizing the intuitive, "folk psychology" understanding of the mind. That, however, is arguably instilled in us evolutionarily (Dennett has argued for this).
The problem is that the folk psychology creeps into everything.
For example, abstracting the parallel system as serial one - the problem is that it is not always possible even though it feels very much that it must be possible. Consider two people trying to turn a steering wheel in different direction - one wants to turn left, other wants to turn right, nobody wants car to crash into a light pole in the middle, the car crashes into light pole. It seems to me that our decision making is much too often similar to this.
Yet we model such incorrect decision making as some sort of evaluation and comparison of options using some fallacious but nonetheless sensible-ish logical-ish rules; rather than the contest of inclination and brute signal strength.
The two people pulling steering wheel in opposite ways end up crashing into the obstacle in the middle not because they are an entity that for some fallacious reasons believes that middle path between two extremes will combine the best, or be a reasonable compromise. Nobody in that car thinks that the car is best off driving into a lightpole in the middle. Yet we address it as a middle ground fallacy and write long explanations why middle ground fallacy is a fallacy. Then it doesn't really work because both sides always knew that driving in the middle is unsuitable and it was the reason why they were pulling so hard away from middle - but sadly in opposite directions.
Now, try to consider a single individual in that position. Given limited time, the brain being distributed system, there will be some disagreement between subsystems, and parts will be coming up with partial solutions to partial problems, which don't work together.