Well, Season 3 was when they were caught up in negotiations with ABC, where they were trying to figure out an end date for the show (and therefore how much longer they'd have to tell the story). Once they established that (an amazing feat, too -- most shows would be left to spin out episodes until their ratings started declining), they got on track, and every episode was not only the next hour of the story, but one less hour left in the series. Everything felt different after that . . .
. . . but yeah, that's why the beginning of Season 3 felt a little padded, but everything from mid-season on has been crazy foot-to-the-gas-pedal delivery. Man, do I love this show . . .