At the moment, the settings.xml is the only place you can specify a mirror at the top-level. It should be possible to have profiles in your settings.xml where you could specify different mirrors.
Consider the following scenario:
Your company has two repositories. The first one contains artifacts for internal development use only (sources of third-party artifacts, their javadocs, etc). The second one is used only for releases and is accessed by externals/partners. Yes, you can always create profiles and have the respective repository sections in there. However it's a lot easier to have this handled by Nexus where all these repositories have been added and just have two wildcard mirrors (according to the profile) - one for internal use and one for external.