Why are chips still built in only a few layers?

Even modern silicon only has some 60 of them right?

Plus don't transformers work in layers, making it natural to put a bunch of layers on top of each other? Regarding cooling, couldn't there be liquid cooling through a plumbing network in the same die?

Our brain takes quite a large volume, and we want chips that have a similar level of parts count (achieved - 80 billion neurons) and interconnectedness (not yet, around 10k synapses per neuron). Why do it in 80 2D layers? Is there no way etch silicon in 3D?