Lost really could have never had a happy ending. Evolving from a castaway drama with an exciting cast of characters and some sci-fi inflections into one of the defining shows of the 21st Century, as it headed towards a conclusion there was no way to please everyone. That's mainly because people wanted totally different things; some were in it for the mysteries, while other for the human interaction.
The sixth season attempted to address this imbalance of appeal by providing an 'answers episode' (the much-maligned Across The Sea) before the entirely character-based finale. As most fans fall into the former camp all this approach didn't really help matters; after we got the answers (the Island is a hub of light or something and Jacob is its protector) people expected a further reveal, some final twist. What they got was, shudder, character resolution. And that's because, for all its Jack vs. the smoke monster, the finale was an ending to the show Lost had originally been.
You see, the show, to the writers and the audience members who steered clear of rampant internet speculation, the central appeal of Lost was its characters. The show's best moments were character based, with the mystery reveals all coming through the eyes of Jack, Locke or whoever's centric episode it was. However, once the intertwining character relations before the crash of Oceanic 815 had been explored to death by the end of Season 2, the less grounded sci-fi elements took off and people tried to unravel the mystery, coming up with theories ten times more intricate than what the writers thought.
Head writers Damon Lindelof and Carlton Cuse didn't help matters by stoking the fan fire by extending the show's life to amp up the mystery and giving purposely ambiguous statements hinting at some plan bigger than there was. But even if they'd stood up and said "the mysteries aren't the central point" people would have just read that as a lie.