I think my favorite way to play capture the flag is with a Mobile HQ's on the map.
The Mobile HQ when done right, has a bonus to init. So each side has their mobile HQ on the mapboard to the rear. If the other side can destroy or "Capture this Flag" and still defend their own Mobile HQ, then they gain the edge on init. Requires good coordination of attacking and defending forces and more of a strategic twist to the game.
-Mek