Because let's face it, the limbo-alt-verse meet up ending could have taken place at the end of season one. Or it could have been the ending to 20 other shows (Quantum Leap, Twin Peaks, The X-Files etc.), it essentially had no relevance to any of the events that took place on the island. The fact that these characters meet up again in the after-life really has nothing to do with the island. Like AT ALL!
It also served to undermine a whole bunch of previous plot elements that now appear to have been red-herrings.
What it did serve to do was give the audience some closure, on the characters at least. Something that The Sopranos failed to do for example.
However it does not change that the show failed to deliver on the core reason most of us were watching, answers to the mysteries! Now I don't care what the writers say about it being the show actually being "all about the characters", because I'm sorry that is bullshit and we all know it! We were not tuning in each week to find out if Kate chose Jack or Sawyer or any other soap opera-esque character development for that matter. We were tuning in to find out what the island was, what the hatch was, what the numbers were all about etc. etc. Sure I cared for these characters, but I was watching the show for the mysterious. And I have little doubt that is why everyone at least started watching the show. Our next day "water-cooler" discussions about the last nights episode were not about character development, but island mysteries.
And for the main question, "what is the island?". They never even attempted to answer it. So it "maintains the balance of good and evil in the world" "someone from Bad Robot" says, AND HOW THE FUCK DOES IT DO THAT?! AND MORE IMPORTANTLY WHY!?!?!? Keeping a plug in a hole is hardly a sufficient method of maintaining the balance of good/evil!
And of course the other (and probably bigger) major failure for me was the needlessly over done Judea-Christian religious over-tones of the last scene. Making the non-denominational church MORE non-denominational would have helped, or not even having it in a church at all. That alone pretty much guaranteed the disappointment of all science-fiction fans and non-christians. It's clear to me that they meant to transcend any particular religion, but the church was far too Christian looking. Especially with the angels standing at each side of the doors of light.
Regarding that scene this is what "Someone from Bad Robot" had to say about the writers intent :-
"The conceit that the writers created, basing it off these religious philosophies*, was that as a group, the Lostaways subconsciously created this "sideways" world where they exist in purgatory until they are "awakened" and find one another. Once they all find one another, they can then move on and move forward. In essence, this is the show's concept of the afterlife. According to the show, everyone creates their own "Sideways" purgatory with their "soulmates" throughout their lives and exist there until they all move on together. That's a beautiful notion. Even if you aren't religious or even spirtual, the idea that we live AND die together is deeply profound and moving."
* This speaks to the biggest issue I take with the ending. Elsewhere he says the show was ultimately about science Vs faith and that faith won. However philosophy even a religious one (see Buddhism and Taoism, most other religious don't have a philosophy, they have dogma's) is based on logic and therefore falls to the side of science. So if the whole shows main intent is to explore philosophical ideas (one of the main reasons I loved the show by the way) it is a betrayal to that intent to decide faith beats science. Because faith (in the context of a battle with science at least) is believing without evidence or in the face of contradictory evidence. Which is the opposite of philosophy.
Let's take a look at the dictionary definition of "philosophy" -
philosophy
the study of the fundamental nature of knowledge, reality, and existence, esp. when considered as an academic discipline.
The definition is almost identical to the definition of science itself! The only difference with philosophy and science is science seeks knowledge via the material world through experimentation and philosophy seeks to understand through logic and intelectual analysis. But both seek truth from direct knowledge! In truth the whole Science VS. Faith is actually Science/Philosophy Vs. Faith.
It seems to me that the show writers failed to actually explore and/or understand philosophy itself.
While it's true that often people misuse the word in the context of religion, (ie. a Christian might say "my religious philosophy is derived from the ten commandments"), the fact remains that true philosophy is derived from what we can KNOW and what can be derived from intelectual analysis. Which is of course antithetical to FAITH.
The question of Science/philosophy Vs Faith (or knowledge vs faith as a more accurate description) is far too often muddled up with a false belief that those that choose Science cannot have chosen a spiritual answer. I take great issue with this as a science loving Buddhist. However I will defer to another great man of science to make my point on this, Albert Einstein -
Buddhism has the characteristics of what would be expected in a cosmic religion for the future: It transcends a personal God, avoids dogmas and theology; it covers both the natural and the spiritual, and it is based on a religious sense aspiring from the experience of all things, natural and spiritual, as a meaningful unity.
and:
The religion of the future will be a cosmic religion. It should transcend personal God and avoid dogma and theology. Covering both the natural and the spiritual, it should be based on a religious sense arising from the experience of all things natural and spiritual as a meaningful unity. Buddhism answers this description. If there is any religion that could cope with modern scientific needs it would be Buddhism.
So the final message of the show seems to be one that I passionately disagree with, that is that the ultimate questions can never be answered. In my opinion that is a defeatist attitude of those that have given up the search. If philosophy proves anything, it is that the answers to the ultimate questions are always within our grasps, although when we are finally able wrap our minds around them, trying to explain them to others can be akin to trying to hold onto water with your fist. In this regards Lost can almost be forgiven in it's inability to resolve the greatest ideas from philosophy. However I feel they really didn't try with the ending they gave us.
In the end I still like the show, and I enjoyed the ride, and for the most part the show explored philosophical ideas in a manner that was true to the ideals of philosophy, it avoided religious dogma and engaged people in questions that few shows succeed to even approach. But in my opinion the ending was bumbled in such a manner that it betrayed the ideals the show seemed to hold onto for so long. And that is why I feel the ending was not only a let down, but ultimately a failure.
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This is also good article going over some of the major plot holes and clears up some of what was answered to a certain degree and what wasn't - 
