My system is simply just this. 1 cap = 1 point. And 1 return = 0.25 points (1/4). These points just act as a mere counter. When 4 returns have been made 1 point goes to the team who returned the flag 4 times.
So if:
Leader team = 5 caps
Losing team = 4 caps
Now if the losing team has 3 returns and manages to return 1 more time they get 1 point which will give them 5 "caps".
It's rather simple, there can be an indicator showing how many returns have been made in the scoreboard if people don't like "invisible" points. I don't mind whichever.
Now you are free to distribute individual points for returning the flag/taking the flag/scoring or whatever as you which, as long as those do not affect the overall team score.
This system is almost the system that's currently in place, minus the frags and deaths of course.