One thing that's difficult for me to remember when I read completed series in one go (like this one) is that these books are written slowly, over time, and sometimes even in response to readers or critics, causing the series to evolve as it's written. While I expect that Baxter had the story largely written out, it's fantastic how every book seems to respond to the criticisms I had before.
Conqueror addressed my curiosity about the Weaver, brought in the Nazi element, and finally, but crucially, reassured me that these prophecies are not fixed railroad tracks that dictate the story.
Navigator is the third book in this series and the inflection point it heads toward is fairly clear from the title and prophecy, though I won't mention it here (to avoid spoilers).
Navigator is also one of the strongest books in the series, I feel; it has the advantage of the setup of the previous two books and uses the recurring themes of duality and love/lust across divisions very well. The duality is also brought to a head in this book and presages the actual overarching conflict to be revealed in the concluding book.
One of the things that I found distasteful in this book is that it necessarily covers the era of the Spanish Inquisition, but I thought that some of the scenes related to the Inquisition were graphic and completely unnecessary other than to reinforce that a bad man was a bad man.
The conclusion of the book also reveals one of the logical holes in the plot; that the past necessarily interacts with the future. A character's decision to do so is a relatively minor plot point in the fourth and final book.
The characters and their story were stronger in Navigator, but due to the denouement and overall thrust of the story toward the modern age and the revelation of the actual conflict, it really suffers in the scope of the series. Like Conqueror, it is not a book that would stand alone on its own at all.