Zach. I can and will answer literally all but three of those questions on the coming podcast.
Annie is a complete loose end and they not only admitted to it but also COMPLETELY fucked up in the podcast by melding 'The Other Woman' and 'The Man Behind the Curtain' in their minds. I will assume they dropped Annie and Goodwin's jealous wife because of:
1. Lack of time (GODDAMN TRUNCATED SEASONS)
2. Unavailablity of thesps.
It's quite possible the individuals shooting at them were also probably intended to be wrapped up as Widmore's men but at the end it would seem a bit ridiculous to have Sawyer and company flash in and flash out just like that.
She probably came from another country, just like everyone else. Jacob who we once thought was a deity, was just a guy. Just as she was probably just a lady. The important thing was, they wanted it to be a mother responsible for everything as previously it was father figures who drove most actions.
And judging from the skeletons in the Source cave, she probably wasn't the first protector either. Not that those skeletons were protectors, just that the battle for balance has been going on as long as humans have been alive, which makes sense since it's probably the source of all life.
Oh nice! Michael Emerson confirm an epilogue with Ben and Hurley as a bonus on the dvd!
DARLTON HAVE MY BABIES!!!!!!!!!!!!!!