I'd say that the "planet of the hats" syndrome which set in during late season two ("Bread and Circuses," "Patterns of Force," "The Omega Glory," and "A Piece of the Action") was the beginning of a serious decline which the budget cuts of season three only exacerbated, so I'm glad that "Spectre of the Gun" took an alternate approach.
Though in S3 they got away from the hats-planet conceit. (Great phrase, by the way.) Granted, there was decline in other ways. Less location, more bottles, worse writing and, arguably, acting. I'm on record preferring much of S3 to the comedy and rut of S2.
I think a difference between LIS and Spectre is simple execution, too. Looking at the screencaps from an aesthetic standpoint its Trek by a mile. And I know people are LIS music fans here, but the unique Spectre score is great.