After a PM to get a better grasp on this question
... I'll take a stab at the "how do I keep John and Aeryn balanced" part of the question. Unfortunately, this has more to do with my love of Farscape and what I like most about it and less about writing.
While I'm a confirmed, die-hard Benaholic, I don't believe that I actively dislike any of the characters. I admit that I don't understand what motivates Noranti, Jool, and a few others, which makes it almost impossible to create three dimensional characters on the page, but that doesn't mean that I dislike them or exclude them from stories because I don't want them "on the set". If I leave someone out it's because I don't know what to do with them.
If you listen carefully to some of the people in the fandom, you can tell that they really don't like one character or another ... or perhaps like a single character to the exclusion of all else. What I like is
FARSCAPE, with all its nuances and complexities.
Actually, now that I've thought about it a bit, I'd have to say that my stories
are skewed by my personal preferences ... because what I enjoy most about Farscape is when John and Aeryn are working as a couple. I adore the 'Butch and Sundance' mode, when they are cooperating in a snarky, ball-bustin' kind of way, each of them contributing their strengths and knowledge to the situation, and acknowledging the things that they don't know or can't handle. And since I like the Butch and Sundance kind of cooperation, what I see are two equally capable, strong,
loving, and without a doubt
flawed human beings on the screen. My future fics probably reveal my bias the best. I envision Aeryn and John as having a pretty typical successful marriage, which to me means having to work at it, occasionally having problems, fights, disagreements, tragedies, and then all the good times. In order to see it that way, they've both got to be balanced, fully-functional human beings, not some half-developed caricature of a person.
So my balance comes from what I want John and Aeryn to have, and from simply watching Farscape. If my betareader says my characterizations are off, the solution is to go back, watch more Farscape, and to simply
listen to those incredibly real people.
Does that answer the question?