What are new and exciting research areas or applications in systems neuroscience?
As Chuck says in his comment, read, read, read - as you do, consider the following factors for your potential PhD:


What topics are PhD projects in available at the universities that you are considering. Be sure to check not only the project availability, but also the research interests of academics.
A PhD is quite a commitment, which topic would light that 'fire' in you to the extent that it could become a lifelong vocation.


As you read, read, read - ask questions of the academics in that field, download their papers and have a look at what directions that particular research is taking.