One of the most popular such ideas is to replicate the brain by copying the neurons and seeing what happens. For example, IBM's Blue Brain project hopes to create an entire human brain by modeling it neuron for neuron, without really understanding why brains work or why neurons do what they do.

No, the Blue Brain project (no longer affiliated with IBM, AFAIK) hopes to simulate neurons to test our understanding of how brains and neurons work, and to gain more such understanding.

If you can simulate brain tissue well enough that you're reproducing the actual biological spike trains and long-term responses to sensory input, you can be pretty sure that your model is capturing the relevant brain features. If you can't, it's a pretty good indication that you should go study actual brains some more to see if you're missing something. This is exactly what the Blue Brain project is: simulate a brain structure, compare it to an actual rat, and if you don't get the same results, go poke around in some rat brains until you figure out why. It's good science.