I have a feeling that part of the problem with this episode was that a) we still haven't seen the two-hour pilot, and b) it aired out of production order. Going solely by what I saw in the first three episodes, I didn't quite believe Jayne's behavior at the end, when he knocked down the statue and yelled at the mudders. Might this apparent streak of self-loathing be tied to something that happened in the pilot? Likewise, the subplot involving Kaylee and Simon didn't quite ring true. There was that little bit in "The Train Job" where Kaylee and Inara talked about how Simon would like Kaylee's hair, and maybe, maybe a iota of flirting between her and Simon later in the episode, but nothing to justify the level of flirtatiousness we saw between them in "Jaynetown." I have a feeling that something happened in the yet-unaired "Shindig" that would explain it.
The subplot with Inara and that kid she deflowered was kind of pointless. I think Shack said it best in his TWoP recaplet: "Inara teaches a guy that sex doesn't make him a man. She teaches this by having sex with him, and then explaining that it didn't make him a man." I'm also of the opinion that it strains credulity to believe that Inara and the Serenity crew would get totally unrelated jobs on the same backwater planet at the same time. It's possible, I suppose, that Inara made inquiries and got her contract after Mal and the gang got theirs, but it didn't seem like the kind of place that would have a large potential client base, and the kid's father clearly wasn't a former client. Maybe there's a space hooker database, and the father just contacted the nearest one, who happened to be Inara, because she was already headed there because of the other job? I don't know, but it seems a bit too convenient for me.
And finally, the "River is afraid of Shepherd's hair" subplot. That's just weird. I did like what Shepherd had to say about faith though.
Aside from the scheduling issues, which I'm sure Edlund had nothing to do with, the problem I had with "Jaynetown" was that it suffered from too-many-characters-itis. Two of the four subplots (Simon/Kaylee and Book/River) were completely superfluous, serving no purpose other than making sure all the actors got their own little scene. That approach doesn't really work on a show with nine main characters.
A quick word about the dialogue: "gorram" grates on my ears. I'm fine with "rutting" and with the Western-speak, and even with the Chinese (though I'd like to know what's being said), but "gorram" just doesn't work. I understand they can't say "God damn" but why not just stick with "damn"?