I've noticed a huge trend amongst players over the course of the last few titles to circle jerk flags for the boosted gains. Leaving no regard to the flag immediately being retaken as soon as they leave radius. Just on to the next batch of points. To me the higher the points you get for capturing the less incentive there is to defend them.
I propose that the winning "Team" receive a smaller overall win bonus (50% less than current) and a 4x bonus on their individual flag defense points.
e.g. Total flag defense score x4