I think this is a very interesting topic to write about, and a good source of discussion as well. Like you say, there are a lot of different directions that you could go with this, and I guess a lot of it will depend on how you interpret the characters. Personally, I have a hard time seeing Jillia as being very open about any negative feelings she would have. She was someone who obviously dealt with a lot of pain in her life, but seemed to bottle it up for the most part. There was a sort of self-sacrifice about her as well, in that she was willing to essentially submit to Jowy and act as a willing pawn because he convinced her that he could stop the war. It's not really revealed until almost the very end that Jillia was at least partially motivated by love for Jowy, a revelation which I think even took Jowy by surprise. We never really get to see the development of that relationship play out, since we only see little snapshots of Jowy & Jillia's time together throughout the game, so that's certainly something you could interpret and expand on.
All that being said, Jillia would have plenty of reason to resent Jowy as well, and though she may not be as forthcoming about those feelings at first, you definitely have plenty of room to explore them and decide how Jillia would express them. I can see Pilika being more blunt and forthright than Jillia, and it's possible that Jillia could put up a brave front, but Jowy would become more aware of her feelings through Pilika.