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As I recall, the main point of contention was that this was one of the first big “there’s a big mystery and the whole series is one big story to unravel it and we totally have it all planned out, honest” series. And then it turned out that no, they didn’t totally have it planned out, and they were just making crap up as they went and most of the profound “clues” people were trying to cobble together were basically meaningless.
Maybe the show runners managed to cobble something together out of them that was satisfying regardless, but still, it felt like quite the betrayal. History repeated itself with Battlestar Galactica, where the show kept insisting “they have a plan!” When no, they really did not.
Something similar happened to Babylon 5, it was designed as a 5-season series and then they were told season 4 would be the end. So they hurriedly wrapped everything up for the season 4 finale.
And then they were told they were getting a fifth season after all once that was all locked in, so they had to create a whole season of filler for season 5.