I was thinking that you could do something like making it very simple and easy to get to your opponents flag but when you got there, you pressed a switch. After three minutes of defending or whatever, a door opens, you grab the flag from the little room, and quickly get out. You could even set the door to close again after like fifteen seconds and make it so you can't camp in there so that if you don't get the flag successfully back to your base then you have to do it all over again. I also like the idea of a infection game with multiple levels and having the end level a great defense position but every room you are locked in is harder and harder to defend until that.
I used timed map events big time in my fallout map. Two minutes in to the map, the stage transforms totally. About five new buildings appear, the effect gloomy appears, and bombs drop, so everyone hears it like the bombs dropped in fallout. Its very neat.