First off, make the flag drop button drop them one at a time, starting with your flag if you have it.
Second, make the default winning score 3 'captures'.
Then, alter the way points are scored -
one cap if you deliver both flags simultaneously,
two capture points if you only deliver the enemy flag, whilst yours is in the holder.
Optional extras include: making the return of your own flag worth a few frags, or a medal; only dropping the enemy flag when you grapple/translocate; being able to carry your own flag in any vehicle.
All of the above force teamwork by making it easier to win if your base has been properly defended (they haven't taken your flag) or no-one's been a flag hogger (despite how cool it looks to have crossed flags on your back and a dirty great sword in your fist). Also encourages retrieval scouting, as one of your team zips in and out to retrieve your flag on a hoverboard, in the face of most of the enemy team who want it for the points; the scout can also keep them distracted whilst his team go for the cap

Of course it won't be long before some enterprising so-and-so figures out the 'last second handoff' technique, which may need to be discouraged, perhaps by a speed penalty for having both flags.
That's it I think. Thoughts, comments and exuberant adulation all gratefully recieved. If I come up with any more I'll add it later.