The main weakness of Rough Beasts is perhaps the quite clean division of its plotthreads. On the one hand we have Spock, his reunification movement, the developments in Romulan space and the founding of the Typhon Pact, on the other a Sisko who somehow reverted to the beginning of DS9 in attitude, self-esteem and approachability perhaps.
Honestly, I never quite understood the rationale behind Spock's reunification movement. I don't see it leading anywhere but perhaps an approachement between the Romulans and the Federation at most. I even consider the idea of spreading Vulcan philosophy a bit arrogant, as though the Romulans are lacking in some way and need enlightenment. Granted, he doesn't force his views on anyone, but the whole idea just sort of sits wrong with me.
In this novel, though, the reunification movement is just a means to get an inside view of Romulan politics. After intrigues, assassinations and political smalltalk the 2 Romulan states come together again under one banner and a praetor who values political discourse and candid opinions. But she's not the one holding all the threads. At least Spock's now in a position where his involvement with the Romulan supernova becomes possible.
As to who's holding the threads... each of the Typhon Pact member has its own agendas, the Tzenkethi are afraid of the Federation and want a strong pact to oppose them, but not a Typhon Pact that's controlled by the Romulans. Therefore they manipulated Romulan internal politics without their knowledge to get a praetor that's most suited to their wishes (though to me they were quite suspect when Xarian Dor remarked on the handshake during their meeting). But what exactly it is that they fear remains in the dark - even in Sisko's flashbacks which tell of the cruelty they're capable of and the fear that they themselves instill in others, but which don't shed light on their motivation. Is it a fear of being controlled? A fear of being contaminated? After all, they are masters of genetic manipulation - do they fear those who are "bred naturally" and advance on their own means?
Speaking of the Tzenkethi leads to Sisko who fought during the Tzenkethi war. But what was that war actually about? I also didn't quite get the reason behind that rescue operation when Assurance fell towards a planet. If shuttles are capable of towing a ship out of a planet's atmosphere using the ship's own tractor beam... why can't Assurance's own shuttles do that? Maybe they were busy evacuating the crew onto the planet, but I don't remember any mention of that.
That leaves Sisko himself who is once again torn between his role in the prophecies (paraphrasing: If you marry Kasidy you will only know sorrow) and leading his own life. In the end, he sort of does neither. He isolates himself as best as he can from his loved ones, and inadvertantly lives and brings the sorrow he sought to prevent. In a way running has always been a part of Sisko's life. After Jennifer's death he took a posting on Utopia Planitia (certainly to be able to care for Jake, but also to get away from open space), after Jadzia's he ran to Earth, so it's not a new concept of punishing himself perhaps. On the other hand, as much as he claims to no longer have any connection with the Prophets, he's still very much their puppet. He once went against their wishes leading the armada in "Tears of the Prophets" - and Jadzia died in his absence and the Temple closed. He again went against their wishes in marrying Kasidy and after his return from the Celestial Temple there's been a rise of fateful events, the kidnapping of his daughter, the death of friends, the Borg invasion and his return to Starfleet followed by Elias Vaughn's being essentially brain dead (BTW, why's he still kept alive on DS9?!?), his father's death, his being unable to contact the Prophets... all of which leads him to believe that that sorrow is upon him and he has to protect everyone from suffering with him. I understand that - on the other hand, he takes away something essential from those around him: the ability to make their own choices.
A few other things:
* Kira is a Vedek? Oh, I'd love to read more about that (though perhaps that was in another DS9-relaunch-novel which I stopped reading...)
* Is Sela now still the head of the Tal Shiar under Kamemor's leadership?
Hopefully, the follow-up duology will answer some of those questions.