I have a copy of Allegiance in paperback, but I haven't gotten around to it yet. As for the rest of your comment, well... I can only respond to that in respect to what I've seen in the Republic Commando books. And in those, yeah, well, the Jedi pretty much -are- screwing over the troopers and the Mandalorians -are- supposed to be the "good guys" insofar as there -are- any good guys.
Granted, just in general, most Mandalorians are not nice people, but admittedly, they do have a pretty interesting set of traditions and I find them, as a people, to be worth reading about, so I don't see anything "wrong," per se, with making them such a big focus. Though, to be fair, you're not the first person I've heard who's accused Traviss of babying her Mando characters too much, even at the expense of the Jedi characters.
So yes, in the other novels (i.e. those not set in prequel era) she's written, it's entirely possible that Jedi characters are portrayed... poorly. I wouldn't know. But for the stuff I've read, and for the reasons I've read them, they do the job.
As for what happened to Mara, well... don't get me wrong. She's without question my favorite Expanded Universe character by far, and to have her go... especially the way she did... I'm not a happy camper. But, I imagine this more has to do with the folks at editorial than it does individual writers.
And yes, you'd better believe I've read the Wraith novels. Among my favorites. :D (Ton Phanan rules all.) I basically stopped after Del Rey lost the license and ended the NJO stuff. Everything after that has been pretty much hearsay.