I disagree on running back with the FFC to protect him. It will only result in a wave of enemies into your base immediatly after you cap.
Staying and keeping respawning enemies busy for a few vital seconds, is far better
Not so. It's more important to protect the FFC and ensure the score. The theory behind this, of course, is that as long as the FC hasn't scored, it's possible to kill him and return the flag. In other words, if your base is swarmed after you score, and they grab the flag, you still have a pretty good chance of returning it. That's the same reason that you need to protect the FFC - clearing the enemy base doesn't ensure his safety.
