I think another way to put what DavidL is saying is, when you get to that point is you have outgrown MCE...
(It is my opinion) That starts then getting into the next 'level' where products such as MainLobby, CQC and others play. They allow a great deal of control over the av experience and are (in many cases) designed to be run separately from the main display.
I started with MCE and really liked it (aside from a few minor items) and am now in the process of trying to use Sage and CQC as I want (for example) a touch screen to select the music and movies (among other things).
EDIT: I think the other thing you may want to look at is XBOX 360 extenders, although it may not be exactly what you are looking for. You may want to clarify why controlling the single instance is important from multiple locations (as most want to instantiate multiple instances in multiple locations).