Part of the confusion arose from the fact the "puppet master" turned out to be a guy with a God complex who's turned the island into his own private purgatory, primarly for himself, not his candidates, in a quest to correct his own mistakes and deal with his own demons. A lot of people seem to struggle to separate the Island/Light and its purpose (which remain mysterious) from the purpose Jacob, struggling with his own demons (including loneliness, Jacob strived to surround himself with flawed people like him, he had to believe by watching them turn their lives around that he too would succeed in correcting his own mistakes), put him to. It's not before seing the scene from Ab Aeterno again in Aloha that I realised Jacob had a really different vision of the Island's purpose than mother had, and Hurley will have yet another vision (Hurley like Rose is likely to see the Light as something meant to help and protect people who need it and want this help.. which ties in with a main theme of the show that your need other people and they need you, if Mother was right that the Light is some kind of divine essence present in all souls).

I think the writers saw in Jacob's "purgatory" just the most significant example of human beings making decisions that impact on other people, doing things to other people, good and bad - which was a core element of the show, but a lot of people seem compelled to find some kind of divine design behind all this, turning the Island into Purgatory. The writers thought they had dealt with that clearly with Jacob's back story, by making him human and flawed and putting emphasis on the fact everything worked as it did because Jacob had decided it'd work this way. If the show had any pet peeve to fight, it was rather modern excessive individualism.