Here's an idea. Build a level around a single base with both flags. The only way into the base is if four (or pick a number) teammates from the same team hop in tubes. If all four make it in the tubes, triggers open the doors and you score a point or maybe four. If less than four make it in the tubes, they are sitting ducks for the other team.

It would encourage squad-based gameplay and make things more tactical. You might want to make it release teams all at the same time as well, to further encourage sticking together.

Pretty sure you would need to force trigger zones to the client for this to be possible.