Yes...this has been asked before, but it is a really good idea and it wouldn't be too difficult to implement I suspect...
LimeWire used to have an option like this, where you could connect to "your" part of the network based on location or interest. This didn't work at the time because nobody used it and left everybody in the "main" area....

And indeed as you say, supernodes should connect freely and should NOT have this feature.