It really hit its stride once Brian Austin Green showed up, and by Episode 7 ("The Demon Hand" with the T2 retcon and Summer Glau dancing at the end) the show was off and running. Season 2 is sheer genius, although Fox did screw it up a little bit by demanding standalone episodes that had nothing to do with the story being told and that were intended to grab new viewers who hadn't been following the whole series. So a few episodes in the middle of the season will have a bit of a, "WTF, why am I watching this?" feel, but Josh Friedman had to play ball with the network, and once he got them off of his back, he brought the series home in a big way. The last few episodes are some of the best television I've had the privilege to watch.
Glad you liked the first season, and I expect you'll enjoy the second even more.