Well, "The Quality of Mercy" is more of a stand-alone episode (even if some of its plot carries on later.)
True, and in a show like
Babylon 5, the stand-alone episodes must have been tough to write. If I were in charge, I'd want these episodes to be either really damned good or, at least really relevant. I don't find "The Quality of Mercy" to be either. Yes, it does introduce the alien healing device, but in my opinion, the parts with Steven and Laura/Janice should have been more of a B-plot. I also think that it would have been better without Janice. Then we could have gotten more of Stephen vs. Laura, without the Stephen/Janice bits (I never really liked the two of them, especially since it's never mentioned again. Character arc wise, if you take out the Stephen/Janice relationship, where it was clear that they liked each other, but had the issue of Laura in the way, it works better for Stephen.
That leaves the Stephen/Mariah ("The Long Dark") relationship, which was kind of creepy, seeing as how, from her perspective, she was newly widowed and Cailyn ("Walkabout"), who used Stephen and, ultimately, just wanted a fling before she died.
Which brings us to Stephen/Number One, which worked because it was just a physical thing. Without Janice, the relationships we see Stephen in add to his ineptitude. With Janice, he's actually seen as somewhat charming, once he no longer has to prove he's right. To me, this goes to show that Stephen could have had a healthy relationship. I prefer to view him as more of Geordi, inept in relationships, which, again, is why Stephen/Number One worked so well, as he didn't have to try at the relationship, he just needed to be good in the sack.
Which adds to his friendship with Ivanova, as she, like him, is just not cut out for relationships. It also adds to his friendship with Marcus, his opposite, romantically, as he probably would have been great in a relationship, if he'd actually had the opportunity (and pursued it). Marcus sees Stephen as having the means to have what he wants, but just not the ability to handle it. This also goes to Marcus', "Touch passion" speech to Franklin.
For the TL;DR crowd: The alien healing device should have been a B-plot, Stephen is inept at relationships, and hitting it off with Janice (especially at the end) kind of ruins that a bit.
In discussing this, I've come to a realization: As much as I like Stephen Franklin as a character, I never truly warmed to episodes that center around him. I think pairing him with Marcus in season 3 and 4 really did wonders for his character, as I liked that portrayal of him better than I like the ones in Franklin-centric episodes like "The Quality of Mercy" and "Believers."