Under the current system, the winning side gets a modest number of perk points (Is it constant? Never really paid attention), and the other two sides get zilch, although they probably worked and fought just as hard, if not harder, than the side that won the reset.
How about this? Each side gets some amount of perk points after a reset depending on where they placed. Each side's base points would be a function of planes shot down and planes lost, scaled to fall between a set minimum and maximum value. Then apply a multiplier, with winning side getting the highest multiplier, the reset side getting the lowest.