I don't see why you would need to choose at all tbh. I just believe a national tournament of the size of the NC drags on for too long while effectively excluding a part of the community, which a regular clan tournament doesn't.
But you could also totaly plan a shorter nation tournament in between two big clan tournaments, with maybe a limited amount of nation taking part based on activity (a but like the Six Nations tournament for Rugby) so that you guarantee a maximum of competitiveness between the nations involved without excluding anyone for too long.