I have to agree that there are a lot of different ways CTF can play out, and even custom maps have barely scratched the surface of the possibilities. The biggest problem with changing the way CTF plays in TF2 is it's much harder to communicate to players what they need to do differently. With CP mechanics, this tends to be a little bit simpler, particularly in A/D maps. Players just have to find an unlocked CP to stand on for a little bit, and usually arrow signs suffice for direction. In CTF, players tend to get all manner of confused when the capture zone is in a different location than the intel.