SF came along first, and was targeted at IT professionals taking care of servers/networks and has built up a great community. The problem though is that the majority of the site is dedicated to server related questions/problems.
Network professionals didn't tend to frequent the site or consider it a valued resource. NE was started as a place for network professionals to address network questions specifically without having the extra "noise" of questions/answers that weren't necessarily of interest to them.
Is there overlap? Absolutely, and that is often the case within the SE community. Ask Ubuntu is a subset of Unix & Linux which can also overlap with SF. Heck, when you get down to it, there isn't anything you can ask on SF that wouldn't be on topic on Super User.
Neither should the SF community remove networking from their scope. There are many places where the systems administrators will also be in charge of the network. It makes sense for them to use the community that they may be most comfortable with personally. The same is true for Unix/Linux questions.
Since the NE site is still new and in beta, your assertion that SF has a wider user base and more activity is true. However, the counter point is two fold: first that the extra activity could allow a question to more easily "fall through the cracks" and second much of their user base is quite comfortable with servers but not as much with networks.
Here at NE, the user base is clearly network oriented and as long as we keep getting content and users, eventually we will be the clear choice for professional network questions. Until then, I would tend to say the network answers on NE tend to be of better quality than those provided on SF, but SF may often produce a faster answer.