the question of what happened to Claire
That was a big mystery and one that was left for all of Season 5 for them to play on later.
My question is, during her absence, how did you expect they would explain it? I thought that when she appeared in Cabin Fever she seemed like she'd gained some kind of knowledge, and Christian wasn't yet revealed as the Man in Black/Smoke Monster. So, especially when time travel became an element in Season 5, I thought maybe Christian had taken her on a special just-the-two-of-them, time-travel-on-the-Island trip, which was going to show Claire as knowing some key answers in the final season that would help save them or something. I can't be more specific, it was only my vague thought in that interim, and clearly I was very wrong, which is fine.
Just curious as to what others' might have been.