The two seasons of the series largely constitute two different stories, and they're worth treating separately.
This series, you must understand, deals with one of JMS' favorite tropes: The Great Plague. It's a concept that obsessed him for some years -- it was a major concept in B5, central to Crusade, lurking in the background of Legend of the Rangers, and it is the front-and-center main concept of Jeremiah. This story takes place fifteen or so years after The Big Death, a plague that hits sometime around now and kills everyone over the age of puberty. This is the world of the kids who survived, who have grown up and are now trying to rebuild something resembling a normal society.
Season 1 is largely Jeremiah (Luke Perry)'s quest for his father, who had implied, as the Big Death hit, that the family would be safe somewhere called "Valhalla Sector". He continues to hold out hope that his parents are still somehow alive, somewhere. In the course of this search, he encounters and befriends Kurdy (Malcolm-Jamal Warner), becomes involved in the Thunder Mountain project that is trying to reunify the towns, and generally gets into trouble. It's a typical JMS first season: a little slow, with lots of stories that appear to be unrelated but are clearly setting things up for later. In true JMS fashion, the common assumptions aren't quite right, and revelations come at season end.
The second season begins with the aftermath of the previous, and then moves on to the larger, and frankly far better story. Thunder Mountain meet their opposite number, and begin to realize that there are multiple ways to rebuild society, and not all societies are benign. Most of the season consists of the buildup of the inevitable conflict, as two views of the future bump against each other.
Perhaps the best thing about Season 2 is the addition of Sean Astin (of LotR fame) as the mysterious Mr. Smith. Smith is a man who talks to God; more importantly, he listens. He is reluctant prophet, trying to be effective but too often feeling like Cassandra in a world where most people feel like God has abandoned them. He's basically a nice guy, never quite clear on whether he is blessed or cursed by having the voice of the divine always in his ear. As always, JMS injects a complex and ambiguous religious note that defies simple categorization.
Season 2 also grounds the story on a more human level. Whereas the bad guys of Season One are almost X-Files-like in seeming deeply mysterious and all-powerful, Season 2 brings in Jeremiah's personal nemesis, Gabriel Sims. As feral and intense as Jeremiah tries to be down to earth, Sims proves himself both ruthless and clever, even wise in his way, an adversary as interesting as the protagonists that he is laid against. Sims and Smith round out the cast, giving it much more depth than it initially had.
Is it worth watching? Yes, with the caveat that this is a notably truncated story. I will say this: knowing that the series was over, they do bring it to an end. The ending isn't wholly satisfying: it is clear that this tale was originally supposed to go a lot longer, and I can feel that there are a lot of threads that either didn't play out, or got pulled together so quickly that they fall a little flat at the end.
Still and all, it's an interesting story, with many things to say and a lot of good writing, especially in the second season. If it had played out as intended, it probably would have been quite good, B+ or better. As it stands, I'd probably call it B- overall -- a very good story, marred by some structural flaws and an overly fast wrapup.