I feel like the New Frontier time-jump was far less successful than the DS9 one. The DS9 jump was at least motivated by external factors (no more leaving DS9 out of cross-overs), and even though it took forever, all the blanks were filled in artfully enough that if you read the books straight through now, it might almost seem like it wasn't a creation of circumstance. The NF jump was meant to shake things up by restoring mystery to the characters' backstories, but it sacrificed all the inertia the series had, none of the new mysteries could be that interesting (since if anything really juicy happened, it'd make more sense to have it happen within the narrative, after the time-skip), the subsequent novels tended to be repetitive (were there two or three times the Excalibur had to travel to another dimension to fight evil pan-universal invaders?), a number of plotlines and character arcs were stuck in holding patterns, and the sexual relationships got, like, Dan Simmons-weird and uncomfortable. Which is why whenever I hear someone is starting the series, I recommend they treat "Stone & Anvil" as the series finale and don't continue with any of the later books.
And I agree that Šmrhová never really came into her own the way Choudhury had, and with the Trip's death retcon being hasty and damaging the dynamics of the crew during the Romulan War arc by removing him from the action. The Andorian transporter duplicates weren't "bad" so much as "a nagging, dangling thread."
I don't think I'd say it's the "worst," but I'll also throw in a dishonorable mention for "A Time to Be Born/Die." I remember reading the book and being intensely frustrated that the crew seemed to be so utterly passive throughout the plot. Then there's a scene where the bad guys fridge the guest character Wesley is sweet on, and he flies into a rage and uses his Traveller superpowers to kill them all in revenge, and I actually sighed and said "Finally!" because someone was doing something to resolve the situation, even if it was a terrible thing that was making things worse. Then I got to the end of the passage, and it was revealed that Wesley was merely daydreaming about taking revenge and was still just sitting there, feeling awful, and I felt very betrayed by the cruel tease that some events might occur during this story. Many years later, John Van Citters was giving an interview on Engage, the former official Star Trek podcast, and described that scene as an example of the kind of thing licensing approval exists to put a stop to, so apparently, Wesley actually was going to kill a bunch of people at one point in the book's development and the scene was hastily edited. I'm not saying it would've made the book better to have Wesley Crusher fly into a vengeful rage and disembowel a bunch of... whoever they were... but I do think having him still be provoked in the same way and then just think about it really hard made it worse.
