What exactly are the problems with The Final Fury in terms of the rest of the miniseries and VOY?
The main issue with the rest of the miniseries is that it takes a very different approach to the idea of the "race memory" of the Furies that various species possess. In the first two volumes, it was more a matter of cultural ingraining, a result of growing up with horror stories inspired by the Furies, and could be overcome with a modicum of concentration. In TFF, though, it's treated more like a genetic memory, an instinctive response written into our very DNA, and is shown to be completely debilitating and almost impossible to overcome.
There's also a timing problem relative to The Soldiers of Fear
. It's supposed to be right after that novel, with a character falling through a wormhole from one book to the other; but that book is set aboard the E-D before Generations
, whereas this book is set after "Learning Curve," whose stardate is significantly after GEN. However, a later reference in TFF puts it several weeks after TSoF -- perhaps there was an attempt to correct the timing discrepancy but they missed the initial reference. (Internal inconsistencies aside, this could be easily enough rationalized by assuming the wormhole had a forward time displacement of a few months.)
Also, the book refers to the events of First Strike
as though they took place during Tuvok's tenure under Captain Sulu on Excelsior
(an interesting touch, since that was from an episode that hadn't even aired yet), when in fact they took place 26 years earlier, just after "Friday's Child," while Sulu was still a lieutenant on the Enterprise
and Tuvok was three years old.
As far as overall VGR/Trek continuity: The book portrays B'Elanna as overly Klingon, spouting oaths like "Kahless's beard!" and "Blood of my enemies!" which are completely out of character for her, especially for first-season B'Elanna. It describes Janeway as a former engineer rather than a former science officer. And it misinterprets the metaphasic shield from TNG's "Suspicions" and "Descent" as allowing a ship to survive within a star, rather than simply within its corona.
I actually think it's a good book overall. In particular, it does a great job with the "facing Janeway with an impossible moral dilemma" kind of story that was a hallmark of VGR's first two seasons. But it needed another editing pass to reconcile it with the other books. As it stands, it's an entertaining and thought-provoking story but not one I can really "count" as part of the continuity.