Well, in Fallout you didn't have to help the vault or stopping the Master, or are you forgetting that ending.
EDIT: Of course Irenicus would have came after me, but he would be on my turf and not me being on his. That was a lost opportunity in role playing. You get a stronghold, you could build up defenses, recruit individuals, then when Irenicus does come a knocking then you can trap him and his sister on your own terms.