Sites are shown as a tangle of interconnecting lines, so it's hard or impossible to see whether some sites are connected to others by their lines (due to various reasons such as being hidden behind other big sites, or barely touching other sites, or connected at weird angles such that it's unclear what they are suppose to be connected to).
A simple solution would be that when I mouse-over a site (such that it's domain name pops up), both that site & all it's connected sites (and the lines connecting them) would change colour. Then you'd instantly be able to see what's connected to what. Possibly this should only happen for third-party connected sites, as those are most relevant.