The biggest change in the third season of Farscape was the division of the whole team into two groups, each with a version of John Crichton running around. Scorpius was still hunting for the wormhole knowledge and the Scarrans became more of a threat.
John’s goal (in the later parts of the season) of destroying Scorpius work on wormholes borders on the paranoid, but maybe I just liked Scorpius too much as a character to be entirely objective there. As for the crew, Zhaan died early on in the season (thank god the crazy mystic was gone), a new female member was introduced early on (Jool) and another one near the end of the season (Noranti, another highly annoying mystic, damn).
As a whole the series remained interesting to watch, but the characterization was still slightly off. Too often it depended on characters going a little bit crazy each episode, on screaming and all-around insanity. Maybe that’s why I liked Scorpius above all others characters, he was most of the time rather calm and sane. And he was the villain.