What the character analysis didn't mention, to my surprise, is that Jool had another purpose: she was the viewpoint character, the person who didn't know anything. Crichton had that role initially, of course, but by the time the third season rolled around, Crichton knew the lay of the land, so they needed a new newbie.
One could argue, though, that Sikozu had the same purpose in S4, and they used her to much better effect than they did Jool. Sikozu's arc was integrated better with the Moyans and Scorpy because she had a stake in the Scarran vs Peacekeeper conflict, but she still managed to retain her own agenda and remain somewhat of a wild card. We were constantly reminded of how Sikozu was "still learning" about how the Moyans operated, and she was very much so the outsider, but it was always interesting to watch how she would try to fit in- sort of like a square peg in a round hole.
By contrast, I always felt that Jool felt shoe-horned in because she didn't have any connection anyone in the larger framework of Farscape, be it Peacekeeper, Scarran or even Nebari. She plays the part of the newbie as a window for the audience, but her character only really served as exposition which is fine only up to a point. Over time, she grated because it seemed the writers didn't know what to do with her and emotionally we had nothing to connect with her over.
That's why PKW was so different in terms of the audience's reaction to Jool. Not only were the Moyans revisiting an old friend/ally, she had her own stake in the main narrative because of her time with the Eidelons. We cared when we saw her (maybe?) death, not only because of the history we had with her character, but because she was finally operating as her own agent, with her own agenda. This is what we should have gotten from her in S3. Because from a newbie POV, from someone who watched PKW before watching any Farscape, my brother was able to follow along with Jool playing exposition fairy and still felt bad when she died.
So I see your point and I see where they were trying to do with her character, but I don't think they executed it well enough until PKW. It's sort of a shame Jool died right when she was actually starting to show some interesting growth.
But, um, yeah, topic: Good job with the articles, guys!
