Even though they both discuss the U-869 dives and the Rouse tragedy, the two books have very different points of focus. The Last Dive was about Chris and Chrissy's relationship and the factors that led to their deaths. It also discusses many of the issues surrounding technical diving and the toll that some of the early tech divers paid for their experience. When you read the book, Bernie Chowdhury makes it very clear that one of the reasons for his writing the book was to help him come to terms with his own diving accident. I found the background information and the stories of the other divers to be very interesting and integral to the story that Bernie was sharing.
That being said, I think that Shadow Divers was a better read. The story was more focused on the exploration of the sub and, in general, I liked the writer's storytelling style better.
You've also got to look at the timing of the two books. The Rouses died in October of 1992, and The Last Dive was published in 2000. Shadow Divers was published in 2004. That gave Robert Kurson 4 additional years to put the story into perspective.
The bottom line is that they're both very good wreck diving books. They both impart the sense of adventure that comes with diving an unidentified historical wreck that most of us will only read about. Add to the story a tragic accident caused by multiple factors (competition between a father and son, limited financial resources, bad sea conditions, poor judgement, a siltout, nitrogen narcosis), the complexities of identifying a Nazi sub that was supposedly sunk off of Gibralter, not New Jersey, the issues surrounding diving a war grave, etc., and you've got some fascinating reading in both books.
I guess I don't see much reason in comparing the two books. They achieve different goals and both have enriched my understanding of diving deep wrecks in the Northeast. I can unreservedly recommend both of them, and I think that they supplement each other well (though I would like to know the actual circumstances of the helicopter pickup - that bothered me too.)
-G