I think a 2 country system would be better for  long term 
strategic plans.  And your right, its always 2 vs 1 anyway.  
This is true in real war also, however.  Almost always will 
the combatants align themselves to form 2 distinct adversaries.
  The 3 team system adds little or nothing to the game but 
there is always the 'shifting alliance' factor.  This limits 
strategy to short term objectives, which isnt necessarily bad, 
but maybe short-changes the 'game-within-a-game' 
potential.
  Having said this, its too late to go with less countries.
  The roots are too deep.