I thought the third season was quite good as well, since it finally started taking the main characters in forward directions, getting Chuck and Sarah together for good and bringing Morgan, Ellie, and Awesome in on the secret. The fourth season's plot was long in the tooth, but they continued progressing the characters, so I was happy. The fifth season had neither plot nor character progression, and it was mostly a waste of time.

The final episodes (and yes, it's done-done now) used a bit of a strange twist to threaten Chuck and Sarah's relationship in a way that hadn't been done before. Unusually for the show, everything wasn't set back to happy and the normal course of things by the end. Basically, and if you don't want a spoiler stop reading now, Chuck and Sarah had their relationship reset to zero, marriage and all, but ended on a note that suggested they were going to make it work and rebuild.

There's no more Intersect. Chuck only had the Intersect for part of one episode in the last season. The character had advanced enough that it wasn't needed anymore. But the Intersect still played a role in screwing everyone over by the end.

But perhaps the greatest thing about the final episode was that it had what might be the best Jeffster moment of the series. Though I'm also partial to them crashing the birth of Ellie and Awesome's baby midway through the fourth season to play their music over the hospital loudspeaker, causing Casey to narrow his eyes and growl, "Jeffster."