>>13781123I studied neurons for my PhD; single-neurons, not whole-brain, but it illustrates a bit of the point.
the brain is the most complex structure in the known universe.
We know quite a bit about it; from how it forms during development, the different pathways that get switched on to guide neurons toward their target destinations after neuritogenesis, the eventualy contact and pruning of excess neurons, the formation of synapses, the density of synapses for certain neurons, etc.
There are always unanswered questions in science. Even individual proteins, we don't know how they always interact/what substrates they utilize, and we're now really investigating the different expression levels and uses of some proteins during development, etc.
At the cell level, there is a ton to still discover.
At the circuit level, there is a ton to still discover. But that's true of every field. Saying "we don't know a whole lot about the brain" is a useless statement, and is not in opposition to "we know a whole lot about the brain", because I could easily support those two subjective statements with evidence.
How do you begin to answer a questions "how much of the brain is still a mystery". You have to be more explicit: What do you mean by brain? Do you mean every single protein and every single developmental event? Do you mean a static adult brain and it's full single-cell sequencing, which we now believe certain events during cell-division could leave entire hemispheres of your brain with different genetic alleles? Do you mean what circuits fire during different decision making? Do you mean "how many exocytic events per minute occur under X, Y Z conditions for these specific set of neurons"?
We know a lot. If its about consciousness, it's an emergent property and difficult to predict on it's own right now, but we've been piecemealing it together forever. It's all incremental. You wont wake up one day with a full-understanding of the brain, it slowly will become understood.