Overall it was a good show and an emotional ending that I enjoyed, but I did have a few problems with it.
In "Ab Aeterno," we found out that the Man in Black is the personification of evil who's greatest desire is to leave the island. The island functions as a prison and protects the outside world from his influence. Jacob is his jailer and in order for the Man in Black to escape, he must kill Jacob. Jacob can be replaced by another, thus keeping the Man in Black imprisoned.
That right there explained everything we needed to know to understand the story and the characters. If they had just stuck with that, it would have been great.
Then "Across the Sea" aired and promptly ****ed everything up. First we are told that Jacob and MiB started life as ordinary human beings, and MiB turns out to be a decent person. He is his mother's favorite and loves her, but eventually discovers that she has lied to them about everything and that she is a murderer, so he abandons her. As an adult, MiB has developed a natural curiosity about the world beyond the island and has decided to leave it. His psychotic mother shows up, tells him he can't leave for no reason, attacks him, destroys all his stuff and murders every one he knew after imprisoning them for almost 40 years for no reason. He kills her in response and feels remorseful afterwords, even though she was a dangerous murderer who could not be stopped by anyone other than her sons.
Jacob follows his mother like a lap dog, does whatever she asks without question or explanation, and has no problem with her lying or killing. He states clearly he has no desire to leave the island or even get his own place. He still lives with his mom well into his 30's.
Why is MiB the series' villain and not Jacob? Jacob and his mother imprison innocent people against their will. They require and reward mindless obedience to their authority. MiB is a decent guy who thinks for himself, believes killing is wrong, and his only crime (prior to becoming the smoke monster) is that he wants to escape from a prison he doesn't deserve to be in in the first place.
In the final episode, MiB becomes a man again after the cork is removed by Desmond. Yet he still can't be allowed to leave. Why?
Why can't MiB leave even as a man? Plenty of other characters have left the island, why not him? Why is it so important that he not leave that dozens of other people be murdered in order to prevent it?
Another problem was the island's purpose kept changing. At first it was a prison to contain evil, but then they decided it was actually "the source" and had to be protected from the MiB and the world at large. Yet it seems pretty easy to protect:
- No one even knows the island exists unless the Protector brings them there.
- Even when they know it exists and where it is, the island/Protector must allow them back to the island.
- With few exceptions, everyone who comes to the island wants to leave.
- No one knows that the heart of the island exists unless the Protector tells them about it.
- No one can go to the heart of the island unless the Protector allows it.
- The MiB cannot kill Jacob himself, he needs someone else to do it for him.
Given these conditions it would seem protecting the island would be a pretty easy job; don't bring people to the island, ever. Yet the protectors keep bringing people to the island. Even worse, they make it all but impossible for anyone to leave.
A ton of stuff in the final three episodes doesn't make sense or have any logic to it at all.
What it really is the writers coming up with a ton of plot devices and rather than making an effort to have them makes sense, they just cover it with a lot of meaningless psycho-babble and pseudo-philosophical BS about how its all metaphor, it's really about the characters and the plot and story don't have to make sense, blah, blah, blah.