The file system always has an advantage over any hardware or third-party software solution; it has an exact understanding of what is going on and it has that understanding typically at a better level of granularity. Where the file system can help the storage management process is either by exposing that information via an API set or communicating that information directly to the hardware or software.
There are some examples of file systems doing this today. For example as we discuss in our Thin Provisioning White Paper, thin-aware file systems can communicate directly to thin-enabled storage systems to allow the hardware to reuse deleted blocks. While some storage systems can do this externally, having the integration at the file system can lower the amount of processing work that the thin provisioned system needs to perform and release that capacity in real time. Another example is that some file systems can communicate to backup deduplication devices or software exactly what blocks have changed in the file system so only those blocks need to be examined for redundant data instead of scanning the whole file system.
NAS systems, in order to provide these services, typically must have ownership of the entire storage system. In fairness, when they do have ownership over the storage they provide much of the functionality listed above, but it all has to stay within their ecosystem. They don't typically support third-party storage or communicate to third party backup applications. The NAS file systems that do support third-party storage hardware should now be working on communicating free space or changed blocks to those hardware platforms to further add value to the software only NAS model.
File systems, for the most part, have been focused on replacing much of the storage hardware system's functionality by adding capabilities like snapshots, compression and deduplication. This is good, the hardware vendors need competition. The file system vendors though should look also at augmenting what the storage hardware can do, allowing the user to select what makes the most sense for them.