These thoughts are to some degree related to what other people have posted today. I believe Across the Sea was trying to tell us that "Lost" is not interested in dealing with issues related to origins of the magic on the Island. The Supernatural is just there. What is more relevant to us (as human beings and imperfect creatures) is how we are going to handle such a gift from the Universe if we had it. Are we going to protect it or destroy it? Will it bring the best or the worst of us? One kills to protect it, another one is using it to punish someone else, a third one needs it to leave the island - the Light around the waterfall looked exactly the same as the one Ben and Locke faced when turning the wheel. What came before that is a question you can ask about any religion - how did God came to be? Even in science - what was before The Big Bang? I know some of you would tell me that The Big Bang was an event which made any history prior to that irrelevant to the events after it but what was before it still seems an appropriate question.
With such an approach in mind, I can only believe that Mother was a human. An ordinary human before becoming the Guardian and obviously someone more powerful after that. "Lost" gives us the story of the guarding of the Light for the time Jacob was doing it. We see how he became the Guardian and I guess in the finale we will see how the Light will be guarded immediately after him. How Mother guarded it is a different story. What happens after a new regime for guarding the Light is established is also a different story. And that is why, I think, the finale will be in a sense open. We will see the new arrangement but that will not be the end of the story of the Island and the Light. In a 1000 years there might very well be a new arrangement.
As for the rules - Across the Sea made me think they are determined by the Guardian - MIB told Jacob he can come up with rules when he finds his own game, plus mother somehow made it so that they cannot kill each other. I believe all rules related to the Candidates are thus set by Jacob. Also the rules for Ben and Widmore as inhabitants and leaders on the island - the endless pieces of paper Jacob was sending. What spheres these rules can govern is something that I guess will be addressed in the future. There is a conversation between Jacob and MIB after the creation of Smokey and before Ab Aeterno that we should witness hopefully. Obviously a rule "MIB cannot leave the Island under any circumstances" cannot be created. Also, Jacob might feel guilty for his decision to imprison MIB, so he decided to show him that people can be good and therefore it make sense that MIB and his (evil?) powers should stay where they are. It is interesting that in no conversation Jacob expresses desire to cease the existence of MIB. He might not be able to do it but still all he talks about is just keeping him there.
The big question after this episode for me is whether the Island has a will of its own. If Mother did not bring Claudia to the Island, was it an accident? Who gave the super intellect and the ability to see dead people to MIB?