In tonight's episode there were a few short sentences that could possibly reveal huge things. This is speculation and I'm not entirely sure how everything will lead to this, but these are strong possibilities to describe what we are seeing.
The ALT is not a prologue or an ending. It is a glimpse into what could have been or what could be. Think about it -- Jack has a son, Locke's getting married, Kate is possibly innocent, Hurley is lucky, and so on. Yeah tonight showed Sayid doing some bad things but he was protecting his loved ones and his home girl Nadia is still alive and has feelings for him even if there's this love triangle happening. What brought me to this conclusion? Flocke said himself to Sayid something along the lines of being able to give him what he wants and Sayid replied by saying what he wants is gone. Well what if in some way he could have what he wanted but not by leaving the island? What if when he died/got infected/something we haven't seen yet he gets to see this other reality? The same could go for when Locke died, or when anybody else goes on to die (maybe everyone dies/gets infected in the end). This could be the end, or just an illusion in the middle before everything gets r! eal for the final battle.
More on that in a minute, but first let me touch on something else that was mentioned. Dogen(?) said something about how every person has a scale of light and dark (and Sayid had tipped to the dark). What if Jacob and MIB are not rivals/brothers/old pals and instead are the same person split into two? Think about it, both have supernatural powers and have possibly both shown themselves in different forms across the island. There was that scale in the cave that Flocke threw the white stone off of. What if he did that to symbolize that there was only one side left of the original Jacob? Perhaps Jacob found a way to split away his dark side so he, with control of his body, was pure good. And his other side, smokey/mib was the evil banished from his body. And maybe part of why the loophole was necessary was because mib couldn't kill himself. There are still questions here, but it's a start.
Back to the other part of this theory -- maybe the candidates/people in ALT don't have to die or get infected to see this fantasy world. Maybe the Jacobs both have the ability to project this. And depending on the path you take your fantasy world is different. Or maybe everyone will end up falling victim to some infection/death. I don't know, it's just a thought. But it's a strong possibility we're seeing a fantasy world brought upon by Jacob/MIB and not an jughead result/prologue/epilogue at all.