Last night's episode of Lost, entitled "The Variable" had many revelations. Rather than bring out what they clearly showed and answered, I have only one theory to write about that has not been proven.
I've always figured that Charlotte was Widmore's daughter. Again, a theory with no concrete backing yet, except maybe the similarity in there accents. And I believed that the woman Faraday spoke to about the bomb near the beginning of this season, was his mother (which turned out to be true). Since Widmore is Faraday's father, this would make Charlotte and Faraday siblings.
They obviously gave the impression that Faraday loved Charlotte. But they cleverly mislead us about that love. She is his sister, and he was trying to save her.
The writer's of Lost are big Star Wars fans (thus the "Some Like it Hoth" episode 2 weeks ago). Star Wars lead the audience on, in regards to a relationship possibly happening between Luke and Leia. But it turned out they were siblings. Lost is using this exact same idea, and I'm not sure if we'll get confirmation this season on it. But I feel very strongly that this is the case.
That's my only real theory that can't yet be proven. Many others (and the vast majority haven't been typed on this blog) have come true.
...Well wait, there's one more. Miles will die. Either at the end of this season or next. It would be fitting if he dies in an effort to save his youger 3 month old self and mother from The Incident. If that is the case, we'll find out in a couple of weeks. The reason for this is that all those who Widmore sent to the island to get Ben Linus will eventually die. Faraday died, Charlotte died, Naomi died. Miles is up next. Thus my theory.
Always remember, whatever happened, happened.