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.