Discover magazine has an article on ’10 unsolved mysteries of the brain’ which describes some of the biggest challenges in contemporary neuroscience.
It’s an interesting list, not least because you’ll notice that several of the problems are conceptual rather than empirical.
For example, the list includes ‘What are emotions?’, ‘What is intelligence?’ and ‘What is consciousness?’ that depend on a good philosophical analysis rather than just more data gathering.
In contrast, some of the other mysteries include things such as ‘How is information coded in neural activity?’ which is a problem of dealing with the complexity of the signals and their effect, rather than us having problems with defining any of the problem.
The fact that brain research relies as much on conceptual developments as laboratory work is one reason why philosophers are so important to cognitive science.
I like to think of them as conceptual engineers.
Link to Discover article ’10 Unsolved Mysteries Of The Brain’.