By limits I don't mean limits on what neuroscience can tell of about the structural components of the nervous system. Rather that much of the difficulties involved in interpreting this data is a lack of information about functional principles, that hold irrespective of the specific structural components that make our biology. Here is my reasons for assuming efforts such as the 'Blue Brain' project will not be as informative as might be presumed, even if it's successful. Which I doubt.
Consider the eye. No engineer in their right mind would design an eye the way our eye is constructed. The wiring from the photocells sicks out in front and interferes with light reaching the photocells. This wiring must then be fed through a hole it the actual photocells, producing a blind spot. It's as if our eyes are wired backward, like having wires coming out of the front of your computer monitor and going into a hole in the middle of the monitor to connect to the computer. The point here is that evolution built up function from previous function, and no mechanism existed to throw away functions that were poorly suited for the new functions that evolved. Instead evolution opted for imposing a myriad of smaller corrective measures to bypass the issues of bad construction.
What would this mean in terms of trying to learn functional principles of the brain from experimental neuroscience? For starters, simply copying a functional element of the brain almost certainly involves copying bad design which includes complex systems to correct those design flaws. This wouldn't be an issue if our body actually had an intelligent designer to avoid such design flaws from the start. If we understood the principles it's likely that the operational elements could be copied without such flaws. Yet simply copying every such flaw without already understanding these principles, even if it works, leaves us to simply wonder if getting this function actually requires all these complex elements. Almost certainly most of the design elements would be corrective add ons to prop up a function of something that originally evolved for a different function.
There's reason for even more skepticism about the success of the 'Blue Brain' project. Consider why it is that, unlike most of our biology, nerve cells don't automatically regrow. In order for new nerve cells to be useful, they must grow in response to a needed and practiced function. Simply growing a mass of new neurons in the brain would not in itself provide any training, or weighted responses to existing functions, to make it useful. To be useful they must grow in response to that use. This is why the most promising treatments for paralysis involve getting some small connection, then exercising that connection intensively.
Also humans have developmental stages such that functions can be built up hierarchically. Thus when a baby can't see, the neural learning to categorize visual inputs never develops. Once the brain develops a world model independent of sight, restoring visual function is not enough to restore vision. In the 'Blue Brain' project, how is this brain supposed to learn to hierarchically organize understanding and qualia without the benefit of the developmental stages required for functions to be built up? I don't think it will happen.
I'm certainly not knocking the validity of experimental neuroscience. It's an extremely rich source of empirical data, which will be absolutely necessary in testing our theoretical models. But I don't see it as the source for the theoretical models to be tested. Too much data can be a hindrance to developing good theoretical models.