You did raise an interesting idea though. Given the proper layout of a ctf map, say the intel is closer to the center of the map and not behind the enemy spawn, I could see a setup time having use. It'd be strange and different, but that's not a bad thing.
Or do it the other way around: the intel area becomes unlocked after, lets say 30 seconds so the other team has time to get to the enemy base and get set up. Makes camping the intel with sentry guns a lot harder since you already have an enemy presence.