No, I didn’t forget this thread, I wanted to re-read the book and give the OP some time to get into it and possibly finish.
Warning: I don’t mince words or concepts in the black box. You have been warned. 
[spoiler]I bought the hardback version of Judas Unchained the very day it was released in the UK (paying international shipping, etc, as it wasn’t released in the US until 6-odd months later), I was looking forward to it that much. Like I said earlier, Pandora’s Star was that rare book that satisfied everything I wanted in a space opera: an interesting interstellar civilization that flowed rather “naturally” from our timeline, an implacable enemy, a strong set of stock characters, told from the perspective of the movers and shakers of society (the lack of which irritated the hell out of me in regards to Brin’s Uplift series.) Etc, etc.
Page 618, from the beginning of chapter 13 – that’s where the fun ended.
But first, the minor annoyances: Renne, Tarlo, etc. Boring. Every word spoken about them was a word not focusing on the major, important, interesting characters: Myo, Sheldon, Kime. For those of you who are wise in the ways of Buffy these characters were JU’s equivalent of the season seven Slayerettes. I don’t need to know about Navy security, and I didn’t need to read all that merely to find that Rafael Columbia isn’t a Starflyer agent.
Ozzie. We spent all that time (and the great ending to PS) for mere back-story on the Primes. What, Sheldon, et al, could not have received the information from the Bose motile?
Oh wait: they did, thererby rendering the Ozzie story useless. :rolleyes: Even worse, it gave him a reason to resist genocide as much as he did. (More about that later).
Mellanie. Wasn’t my favorite character in PS, reduced me to wondering how Nigel Sheldon felt about getting sloppy seconds. (The sequence beginning page 601). I couldn’t help but snort when she asked herself if she slept around too much. Huh, ya think? I wondered if she’ll get rejuved as a virgin. (The great unknown in the PS/JU universe - do people do it, is it even possible?)
All right, here’s the major grief I had with this book. Beginning with chapter 13, JU changed from a story about interstellar warfare between two civilizations and became a 300-page chase sequence to catch one creature. The story shrank, became smaller in scope and scale, somehow less important. And I was never convinced that the fate of the Starflyer was more important than the overall struggle between the humans and MLM and the distributed Primes – after all, the Starflyer was headed to Dyson Beta to unlock its people, so the all the humans had to do was wait for the DB shield to fall and nova bomb it. But what about the unknown stars, the dozens of stars where MLM was installing motiles and immotiles?
Once Nigel’s super-quantumbuster did its thing at Hell’s Gateway, it was taken as an given that the Dyson Alpha Primes were beaten, that all mankind had to do was nova 1 star every 30 light-years to wipe out all the Primes, and that MorningLightMountain had no choice but bow to the inevitable. But I never accepted that premise because MLM knew that the shield could be messed with and would be done so once every 1,000 years or so.
So the solution to the Prime problem was completely wrong – the shield wasn’t infallible at all, it could be tampered with by the Starflyer, it could be tampered with by humans, it will be tampered with again. Ozzie’s “OMG, I can’t live with myself if we wipe these genocidal bastards from the Universe” did nothing but give the Primes another chance to break out of the shell. We were told that it would outlast stars, but it was bizarrely resistant to purposeful tampering by “simple” starfaring creatures. It had a “lifetime of the universe guarantee” but failed in the first 1,000 years. Where the hell did the Animonies get this thing – Kmart?
So the solution was stupid. And instead of focusing on solving the problem, a faux moral dilemma was introduced and resolved which resulted in nothing being solved.
And it was done merely to neatly tie up the MLM spinoffs and the Beta Prime dilemma so Hamilton can write a 300 page action sequence that focused on chasing one Prime trying to leave a civilization that is going to bomb it out of existence no matter where it ends up - and since everybody knows it is heading home, there’s no need to capture the thing and perform some elaborate “revenge” project that itself made no sense.[/spoiler]