There were a lot of twists and turns in the story in both seasons, but what I liked about season one is that they stuck to the classified military program and only really expanded the storyline to include cloning. Having all of the supersoldiers have "twins" (sometimes multiple twins) worked very well and allowed for the same actors to play different versions of their characters. In the second season, they expanded the story to have human/animal hybrids and got into secret societies that just got a little weird and took the story on a tangent I don't think they needed to go. Apparently, if the show would have been given a third season the storylines from seasons 1 and 2 would have been merged together.
The show was very well-acted in both seasons and very well-written in the first season. As I said above, the storylines in season 2 get a bit weird, but the actors all did a great job with what they were given. All the actors, from the main cast to the more ancillary characters, played their characters well. The show was obviously the big breakout role for Alba and she was great as a wise-ass/bad-ass character. And, she was not bad to look at either, even though the show did not focus on the fact that she is smoking hot and rarely put her in skimpy outfits. Jensen Ackles particularly did a great job as Ben/Alec when he was brought on as a series regular in season 2. Ultimately I think it was a show that Fox killed off too soon. Even with the weird tangents that the show went on in season 2, there was still room to tell compelling stories. All in all, it was a very good series with a lot of action, drama, and even some humor. It is definitely not a show that will appeal to everyone's taste, but if you like action stories, especially with a dystopian bent, it is worth your time to watch.