What happened to the Dharma Initiative?

There are two things that I don't like about Lost latest development. One is the recurring cases of resurrection: the last one, Sayid, but before came John Locke with two episodes (first when he was shot by Ben, and the second when he was hung although he resurrected possessed by Jacob's enemy). Also Charlie's first "death" when he was hung by Ethan. And don't forget Jack's father, who was alive in Jack's first flash forward.

Christopher Shephard.

John Locke.

Sayid Jarrah.

John Locke.

Charlie Pace.

The other point is the appeareance and disappearence of groups/enemies: the Dharma Initiave, the Others, Charles Widmore, Ajira Airways flight 315 passengers and the last one, Jacob's enemy.

Dharma Logo.

Charles Widmore.