Just a couple of thoughts. I actually took the time to read over the legal document, and the one thing I will say is that his (admittedly very dull to read) description of the machine sounded somewhat like the animus design. (See below for that extract)
On the other hand, it was repeatedly stated that his book was only available through online outlets, no major bookstores were mentioned as means of distribution. Add in that prior to this lawsuit, the book had one review on Amazon, and no mentions anywhere else, and I think we can safely say that this is not a work that got much attention. I can't speak for the quality of the novel as a whole, but it does seem a lot less likely that Ubisoft happened to read a super obscure book and base their video game series on it.
Also beyond the fairly detailed claim about the Animus, a lot of his references to assassins weren't anything like the AC series. They wanted to find a descendent of John Wilkes Booth, to see if they could place him at Lincoln's assassination. Similarly they wanted to try using the tech on a comatose survivor of a mass assassination in Israel. In both cases it was to find the assassins, not a part of some hidden war between two factions. His other claims seem pretty superficial as well, like claiming that because both his novel and one of the AC games very briefly mentions the idea of memory interference if the tech is used on a pregnant woman is somehow plagiarism.
Anyways, for the sake of comparison, here is his description of his whatever-he-called-it:
?The Link is no longer a hand-gripped device.? Allen picked up an assembly from the small table behind the revised dentist chair now used during the Link experiments. The video monitor was now on gimbals, hanging from the ceiling so that it could be comfortably positioned in front of the test subject and yet viewed easily by those monitoring the test. ?We place this device around Anna?s biceps, just above the joint. As you can see, it looks very much like a blood-pressure cuff, except that facing the meaty part of her arm is this one-inch diameter, donut-shaped ring,? Allen continued. ?In the ring we have incorporated all of the sensors we had in the hand-gripped Link.? Allen picked up a bundled cable, with an overall diameter of about three-fourths of an inch, including a high pressure hose, two twisted pairs of wires and a thin, white, coaxial cable. ?At the center of the ring,? he said, ?we attach this special terminator, which is a gold-plated high pressure nozzle. The metal nozzle is held by the cuff tightly against the arm, making a good electrical and hydraulic connection.? ?Attached to Anna?s other arm, at the wrist, is still a standard grounding strap. The ten-volt pulse is applied between the grounding strap and the nozzle. Power to the Link circuit is supplied by one twisted pair, and the data received from Anna?s particle is carried by the coax to the recording equipment over there,? he finished, pointing to an impressive array at a test station against the wall directly behind the chair, adjacent to the door.
Compare to picture of the animus seen here: http://images.wikia.com/assassinscreed/images/f/f6/Ac_desmond.jpg