But, X-Files' biggest problem was that it tried to have a semi-serialized story arc sprinkled in the middle of episodes that had nothing to do with each other - if you watch all the Mythology episodes in order without the monster-of-the-week episodes, any problems the show had virtually disappear until you get to the Super Soldiers.
Lost, on the other hand, is completely serialized, and its major issue is that if it tries to mix things up (i.e. the raft, the tail-section survivors), it has to keep going with it, and in such a "transitional period" like the first part of this season has been, its bound to be not-as-good as the past season(s) have been.
The new BSG is a prime example - after the shocking end of season 1, it couldn't be expected that season 2 would be the same - so the first 7 episodes were "transitional" and regarded by many as not up to S1's standards.