My main remaining nagging questions have to do with Ms Hawking and with Smokey.
And Smokey: what was he exactly? Was he the evil "corked" into the island somehow let loose when Jacob threw his brother into the glowy cave? Why/how did he turn into the monster then? AND: was Mother also a smoke monster? Is that how she killed all the villagers and filled in the well they built? Is that how she knew it was a fate "worse than death" if you went into the light? Was her "original" body one of the skeletons Desmond saw when he climbed down into the cave?
Also: what happened to Christian Shephard and Yemi's bodies? Why did those bodies disappear? As for the whole pregnancy danger thing: I think it was the "incident" in the 70s that somehow changed things. Because Ethan was carried to term on the island. In one of the Darlton interviews, they said something like: "We haven't spelled it out, but it seems children were born on the island in the 70s and then something happened. What could have happened???" I think they alluded to Jughead exploding/Dharma drilling into that pocket of energy.
I still wonder about the vaccine that they made such a big deal about in the early seasons. Was it to protect from radiation/energy damage from the incident? It seemed very important for Claire and Aaron to get vaccinated back in the day.
Why couldn't Widmore and Ben kill each other? I've wondered about that for a long time. Maybe it was because they had not fulfilled their destinies? They both had roles to play in Jacob's endgame: Widmore had to bring Desmond to the island and play his part there and Ben also had a part to play there. It was just not their time to go, so they could not kill each other just like Michael could not kill himself.
In the end, Smokey's assertion that people are all selfish and corrupt was proved wrong: the losties saved the glowy light AND defeated Smokey because they worked together and because they loved each other and trusted each other. I would have loved to have seen some kind of scene of forgiveness/redemption with Jacob and his brother, but I guess it was really not part of the losties story.