Michael Crouch thought that Jesus ben Ananias was the only authentic an allusion to Jesus in Josephus. The parallelism of "woe to Jerusalem, and "woe also to me", and the boulder that crushes both Ananias and the Temple wall at the same time, in conjunction with the prophecy of the Temple destruction, the crucifixion, and the resurrection.
At first I thought this idea was a bridge too far, but the more I pondered it the more it made since to me.
The problem for me with anything involving Josephus is Hegesippus. Hegesippus seems to be the source where the family of Jesus tradition comes from, and he is probably a redactor of Josephus. It may very well be that, to counter heresies, Hegesippus took from Josephus, Tacitus, and Suetonius to craft a pseudohistory of the church that antedated any possible heretic's claim. I propose the account of James the Just and the parallel in Gospel of Peter as evidence. The death of James is said to be what eventually causes the Temple to be destroyed, where he is thrown off a wall of the Temple, while in the Gospel of Peter Peter is in hiding because the Jews believe he will set fire to the Temple. Hegesippus likely had Peter, saw Ant. 20 where James is killed by stoning and believed these were referring to the same history.
Matthew 20:20-28 states that both James and John will be martyred together, and a textual tradition in Papias states that both were killed by the Jews. Not only does this put into question where the idea of John of Patmos comes from, it also begs the question of where this idea came from. Well, we already have a James being stoned to death in Josephus, and Ananias is a variant of Yohanan, and it would be appropriate that the two's respective deaths would begin and end the prophecy of the Temple's destruction.
