I do feel sorry for the fans out there who feel the finale fell short and feel "cheated" because more mysteries were not resolved. I feel sorry for them because I think they missed the whole point of the show.
I felt it was clear from season 1 that this series was about the evolution of the characters first and foremost, and everything else was distant second. The finale brought closure to the story that was being told in a very clear and powerful way, a masterful job. And I say that as someone who is plenty comfortable criticizing the producers. They did get a little sloppy in the final year. They have admitted that they wanted to tell the story of Ilana, and had planned to reveal such minor mysteries as who was in the second outrigger, but as they got into the season, they didn't have the time to do so. That's poor planning on their part.
But they achieved what the show set out to do - tell the story of the redemption of a group of strangers with intriguing and complicated backstories. The mysteries of the island, Jacob, MiB, Dharma, these were all primarily just mechanisms to facilitate the telling of the the primary story about the characters - unique storytelling devices that helped flesh out the background and evolution of each person.
What I find interesting is that a lot of Lost fans WANTED the show to be about the storytelling devices - the mysteries - hence why they were disappointed when all of the mysteries didn't get resolved. It's like being a fan of a show, and loving a character who is just and occasional recurring guest star, and then being disappointed when the finale doesn't close the book on that character - but it was never about that character, and Lost was never really about the mysteries. Of course, they had to flesh out a good deal about the mysteries of the island for the context to make sense, and they really did do that. Would I have liked more explanation of some other stuff? Sure, as I was as intrigued by the mythology as anyone. But I was fine with what they did reveal, since the show wasn't about the mythology. And I felt 99% of the mysteries, even if unresolved on the show, can be pieced together pretty tightly with what they did reveal.
The FST was a brilliant storytelling device to bring closure to the characters, and one they clearly had planned from early on. If you were dissatisfied with the show and/or the ending, I think it may be because you wanted the show to be something it never was - a show ABOUT the strange mysteries on this island. It was a show about redemption for a group of troubled characters, with the mysterious island merely the backdrop and mechanism to tell the primary story.