Note: This is kind of a knee-jerk reaction. I know that. It's not going to be completely coherent. Bear with me.
You were so close. So, so close.
You almost had a great show all the way through. You shocked us, you entertained us, you made us feel for the characters.
Missed it by that much.
1. Religious heavy-handedness
Jack's entry into the all-inclusive non-denominational church immediately raised a flag. Everyone had been acting very strangely, and when we saw that casket, we knew something was about to go down. Then we saw Jack's dad, realized everyone was dead, they were in heaven/purgatory without ever quite saying it, etc. The icing on the cake was the name of Jack's father--Christian Shepard--guiding them all to the bright light. It was just too much. I wanted to groan.
The spiritual theme has always been present in Lost. Locke embodied it for years, until he died, of course. Then Jack took up the mantle. Jacob hung around to give us the religious vibe in Locke's absence. I don't mind that the "man of science" was wrong in the end. I was just a bit disappointed that they went for a safe, Jesus-loves-everyone ending. It reeked of cheese and frankly I thought they deserved more. The whole scene still feels surreal to me. Why is that? Well...
2. Mysticism vs. Realism
The Island, post-season 1, opened us to a world of mysticism. We had the Smoke Monster, the healing properties of the island, destiny, time travel, Jacob, etc. etc. The Island was a wonderful place where special things happened. They were trapped there and it was a stark difference from everyday life. Before the island, the survivors were criminals, doctors, musicians, fast food workers. They were normal people. Slowly, The Island transformed their world into something fantastic. Then the flash-sideways grounded us again. We saw the familiar characters behaving in everyday ways. They still had struggles and they were still interesting despite the fact that they no longer had the mystical Island juju to help them. There was no Jacob. However, in the final moments of Lost we find out that the whole "realistic" world is a construct. It means nothing. It was undone. All of the new relationships and redemptions we witnessed meant nothing at all. They were all dead. Who cares? Lost had pulled the rug out from under us before with storytelling methods like the flash forward, but I had never felt betrayed or like I had wasted my time. I liked the flash sideways. It helped me feel like these characters, though they may be dead in the "real" timeline, might have a shot after all. But nope. The survivors left behind a lot of kids they'll never see again; Jin, Sawyer, and Michael all had children that are now abandoned. They'll never see them again. And the flash sideways world, where they could have addressed that, suddenly doesn't matter at all. Speaking of kids--
Jack's son in the flash-sideways was something of an enigma. We didn't know where he came from til the final episode, we don't know what happened to him after Locke "woke up," and we never find out. Since the flash sideways is a construct, it's possible that Jack created him as a son that he could use to be the father he always wanted. But it that's true, then that means Jack unconsciously has some kind of reign in that construct. So Jack's unconscious mind put him in a relationship with Juliet. Does that go against any kind of real emotion the characters had in the main timeline? we saw there that Jack and Kate wound up together, and so did Juliet and Sawyer. They were very happy, seemingly. The flash-sideways undoes all of that. It negates it. It seems less real than it was. It cheapens the relationships that we cared about over six seasons.
4. No finality in the real world
One huge mistake they made in the final season was showing us what happened in the purgatory world. There was closure there. Everything was tied up in a neat little bow and the white light bathed us all and we felt really good about it.
But who cares? None of it actually happened. I didn't care at all about that world by the time it ended. I wanted to know about the real world. What happened to Claire and Richard and Sawyer and Miles? How did Hurley and Ben get Desmond home? Those are the real questions. Those are what mattered. The focus was on the wrong timeline.
5. Negation of the flash-sideways
Obviously I mentioned this above. We spent a whole season redeeming characters (Sayid, Jin, Ben) and helping them learn and discover themselves (Locke, Jack). There was some wonderful character development. Jin and Sun were together despite the oppressive nature of Mr. Paik. Sayid saved Nadia, just like he always wanted to do, but at the same time he learned to move on from her. Ben looked like he was going to have a happy future with Rousseau and Alex. Jack accepted that there was room for faith in his life and Locke realized that faith wasn't everything. These were all the lessons that they should have learned in the real world. This timeline was what they needed. It was what the audience needed. In those last few minutes we realize that none of this matters because the characters were all dead when it happened. They never learned these things in life. They never got to grow from their self-discovery. They never got to live life their way if The Island and Jacob had never interfered. More importantly, the audience never got closure. What's the point of having your characters redeemed when it no longer matters?
6. The Smoke Monster
The Big Bad of season six was the Man in Black. The Smoke Monster. We were told that The Island was his prison and he could never leave. If he did, the world would be ruined.
But that's it.
At the halfway point, the Man in Black was shot and unceremoniously tossed off a cliff. Bu we never really saw the extent of his power. It never really felt like the world was in danger. We needed to see what he was going to do when he escaped. We need to know that Jacob wasn't lying this whole time. We got none of that. The fight was great, but it ended too soon.
Lost seems to have fallen into a couple simple traps; we never saw any real threat in the villain, and they failed to realize what their audience needed. These simple things would have saved us a lot of frustration... or at least it would have saved me a lot of frustration. The finale wasn't even bad. 80% of it was fantastic. I loved Ben's redemption. I loved the final shot. I loved seeing (almost) everyone again. I just wish it would have meant something tangible.