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Well, when it comes to the Ysalamiri I always thought they were dumb, because Thrawn explains them as repelling the Force and Luke through Mara echoes that in The New Rebellion. And I thought it was dumb that they repel the Force completely. But as Zahn explains in the annotations, plus I think I heard it somewhere else, the Ysalamiri don't eliminate the Force, they just "spread it thin" to such an extent that it's undetectable by Jedi.
Before that, I had thought it tied into the Yuuzhan Vong and the Unifying Force and that the Ysalamiri repelled the Living Force but the Unifying Force remained, which I suppose isn't necessarily mutually exclusive with Zahn's annotation about it. As for the Umbarans, I just thought it would be succinct if what they were doing was the same as the Ysalamiri, but practically applied rather than instinctively. I always thought that what the Ysalamiri do would be something that a Jedi could figure out how to do if he or she tried.
It's kind of ironic that I'm complaining about overusing connections between stories and then complain that the Umbarans aren't connected to Ysalamiri, but I just think it's redundant to have all these Force defeating things. Zahn started the ball rolling with Ysalamiri, and while I think it would be annoying if those get overplayed, to constantly pile on all these supposedly rare Jedi defeating measures with each successive story seems like too much to me. I guess it's not really a big deal. The lightsaber crystal requiring the Force for the lightsaber to function is really dumb though IMO. Lightsabers are technological, not mystical. I don't remember Lomi Plo doing it so I'll have to check that out.
As for Iteration, when he was first removed from suspended animation he thought he was Jaden, then Nyss put the Iteration information into him with the mindspear and he knew he was a clone, then Nyss put him back in suspended animation, the point being to ensure the clone could handle the mindspear.
Edit: I just read the discussion thread for this at TFN, and someone there said something I agree with completely, and not just with this novel but a lot of continuity in the EU in general:
"Kemp recently said something along the lines of valuing a good storyteller over a good writer, and I guess this shows in Crosscurrent and Riptide. The action and in-the-moment narrative is engaging enough, but we never get enough answers, and what little background we do get seems kind of arbitrary. The ancient space station and the cloning facility are good examples of this. The station is Rakatan, even though it doesn't seem to follow what we know about Rakatan tech, and the cloning project is Thrawn's, even though it doesn't particularly seem like something Thrawn would do. If you're going to be vague about the details, why not make the origins of both a complete mystery and let us wonder?"
A lot of the time it feels like "continuity" when it comes to the EU is:
Write the story (or outline).
Leland Chee reads the story (or outline), notices X, Y, and Z are sort of like these pre-existing SW things, recommends to the writer incorporate them into it.
Writer does so sans research.
Viola! Decorative crystals on Anakin's lightsaber hilt are now focusing crystals integral to the lightsaber's function and dependent upon their connection to the Force! The formerly unique artifact known as the Jedi Holocron that Palpatine couldn't for the life of him figure out how to recreate are now a dime-a-dozen, and Palpatine created his own! Getting back on the subject of this book, the Rakata are pretty firmly established as a technological species that use the dark side to power their machines, not the users of organic technology.
The paragraph so perfectly encapsulates what I didn't think worked in the book. The Star Wars galaxy is a vast place where you could write thousands of stories that all have absolutely nothing in common with each other. If you're going to have continuity between stories in terms of Thrawn's cloning facility or Rakatan tech or cortosis weapons or whatever else the EU has screwed up royally in the past, have it be true to its original use and not something you name drop to give the false impression that there's "continuity." It annoys me when a writer is like "well, I've got this material that's lightsaber resistant, and I see that Zahn and Stackpole invented this material called cortosis, so I'll just call it that even though it's nothing like that."