In general, what Pilot and Aeryn have together is really special. They share DNA and have bonded together as they shared experiences working together out of their native elements (like when they worked in the scientific realm to help Rygel, when everyone was off the ship).
We think of Pilot as all-knowing and happy in the service of others, but there's more to him — angst perhaps. He's a deeper individual than the character who just reports what's going on with Moya.
With The Way We Weren't, we got some of the background on Pilot and Aeryn. I'm always happy the more we can examine and explain the Peacekeeper world because the Peacekeepers are the primary villains, and you want the villains to be as rich and layered and interesting as possible.
So this is a great episode in which to catch a glimpse of the world that Aeryn came from, but also in which to learn about the Peacekeeper hierarchy.
As for Pilot, we were able in this episode to bring in a lot of the background that had already been developed for him, but that was unfeasible to show in season one. One of the reasons for this delay is Pilot's mechanics. To delve into his personality in the way we did in The Way We Weren't, we needed his face to be extremely expressive, and we wanted to bring him out of the Moya environment in a flashback to his home world.
To do these things was too much to attempt in season one, when we were just trying to get the Farscape universe off the ground, develop other characters, explain the way things work. This episode opened both the past and future for these characters.