In writing the Voyager tie-in to the Furies mini-series and this novel, ab Hugh really doesn't like the Federation's comfortable post-scarcity social democracy--Wesley's angry rant in his head at the novel's end about the moral emptiness of the Federation is pretty much his own thinking.
Well, that would explain it. It always puzzled me, because it didn't mesh with Wesley's motivations as established in "Journey's End" -- that he'd come to realize he'd just been following the path expected for him rather than discovering his own identity.
From what I remember of his motivations, stated in the large reference volume of Trek novels that came out some years ago, with the three books I mentioned he was interested in seeing (my, perhaps uncharitable, phrasing) what he could do to break down the core assumptions of the setting and what would happen. In his TNG novel he had everyone behave unrealistically (pompously, hypocritically, etc) in keeping with hi view of the Federation; in his Voyager novel he had the ship exile a civilization from the galaxy, violating Trek norms. (And in his DS9 novel he killed everyone, but It Got Better.)