I've finished reading his complete works. Josephus himself seems to have had some loyalty issues of his own, and he also seems to have made the most of his opportunistic nature through the opportunities the Romans granted him to write about Jewish history. All in all, his work is very valuable, as ancient "historians" go.
Those couple of passages that reference Jesus and James are very curious. Since those passages provide a small internal contradiction in Josephus' writings, most scholars now think that either one or both were probably added later, or more likely slightly edited, at least in the primary Jesus passage. There is some evidence that a "less generous" Jesus passage was already there, and it's therefore hard to figure out just how much was added and what was there originally. "If he can even be called a man" is typically considered spurious by all new scholars for the last 100 years. But it's mostly conjecture, common sense, and guessing. It's been done to death on several Websites.
If an addition had been made to be give a more generous reference to Jesus, we can be very glad, it's what would have saved the entire set of books from certain destruction by the Christians. (Some of the early Church Fathers who were very proud of their book-burning capabilities.)
There's another angle, too: that it's not impossible that Josephus added the complimentary phrases about Jesus as a way to explain the current beliefs about Jesus that had already reached Rome very early in the 2nd century. It doesn't mean that he, Josephus, believed them.
Gamaliel