DOM:
Steal what Destiny did in its control mode. Make scoring based on kills, but you get bonus points on kills with flags held.
CTF:
Make defending more viable by creating a 20 second protected flag status after killing an enemy carrying your flag and returning it to your base. During the protected flag status time you would still be able to capture Flags by bringing them to your base but no one would be able to take your flag away. The 20 second duration allows for your teammates to respawn. It would at least make defending more important, and hence would hopefully lead to a higher emphasis on fighting and less on just running flags.
“There is nothing either good or bad, but thinking makes it so.”