Mild spoilers ahead...and I do mean minor.
Like or dislike Boba Fett, Karen Traviss has a mild obsession with the character so he's here to stay. Still, she weaves his story in very nicely, and I see the Mandalorians becoming more that that third cog in this war wheel.
I agree that much of the series, and this book is no exception, ignores key characters - namely Jaina Solo. Court-martialed or not, I just don't see her doing "nothing" about any of the events.
The Ben and Mara moments, specifically surrounding Ben's reaction to certain book events, are touching and pretty realistic for Skywalker family dynamics.
Allana's an unknown at this point; so, for all practical intents and purposes, is Tenel Ka. I've made no secret in any of my reviews that I've disliked what they've done with her character. She had such potential to be so much more, but they shuffled her away to the plushy prison called Hapes to be queen, while the galaxy spins out of control. BTW, where's Tahiri, Zekk, Lowie, etc.? Yeah, yeah, they've got lame excuses to be doing this and that, but honestly, it's like all the Jedi are gone again.
I've got my own wild speculations about what's going to happen in the future books, but I'm happy that - spoilers aside - Karen Traviss throws in some nice plot twists. One comment about the name picked for Mr. newly patented Sith: it really ought to have been better explained. I'll be naively hopeful here and assume they're going to explain it later, but the ending was just plain "cheesy" - dumb - silly - whatever - blah- ish. One thing I tend to like about Star Wars EU books is their penchant for giving just enough backstory. I know the name was chosen in a contest, and I've got nothing against that. There should, however, be some explanation for Mr. Sith choosing that particular name. Some piece of lore, history, whatever to make it make sense.
Negativity aside, Sacrifice is definitely a well-worth-it read.