First, watch this
http://www.liveleak.com/view?i=a13_1342720681
In most cultures and especially a few hundred years ago during the enlightenment, it was considered honorable for defeated opponents to meet with the victor and discuss terms of agreement and surrender with dignity.
How about for storyline purposes, each faction has a Regional General for every continent. When one faction manages to beat control a continent, a ceremonial victory event happens where the victorious army marches all dressed up with their marching music playing, their regional general leading the group, up to where the Generals who lost await to accept his victory.
Similar to this
It doesn't even have to be a CGI cutscene, with some extra artwork and animation it could be entirely possible to add some extra flavor to the game.
Also think of how cool it would be having every losing player locked in formations only able to move his camera watching the winning army strut on in?
Galaxies of the winning army could also fly over. It would be a great "In your face" moment and in my opinion, the ultimate reward for a victorious army of players who likely would have fought months to achieve it.