What do you think that would achieve? Let me tell you, it would isolate the referees in their own hemisphere based competitions, and widen the gap in interpretations between them. Sooner or later, we have to end up with NH and SH referees at the world cup, and we already have big enough differences now, without making it worse.
What really needs to happen is, not only to have NH referees in the 3N and SH referees in the 6N, but there should also be NH referees in the Super 14, ITM Cup, Currie Cup and Vodacom Cup, and SH referees in the Aviva Premiership, Magners League and Heineken Cup. If they had an exchange system set up so that, say, 10 referees from each hemisphere exchanged places each season, it wouldn't be very long before it wouldn't matter where referees came from because they would all end up singing from the same hymn sheet.
When Wayne Barnes came out to NZ last year, he refereed an Air NZ Cup match between Wellington and Southland. He reckoned he learned more about how the game is played here from controlling that match than in any test match.