Well, you're starting out from a false premise, in that the novels, comics, and video games are not "canon." Only the television episodes and movies qualify for that designator. Everything else is "extra," "gravy," "additional toppings," etc.
As for consistency between the novels, comics, and video game(s), it's important to remember that each of these ventures does not necessarily appeal in a broad way to the same audience. There's some overlap amongst the hardcore fans, of course, but that's a very small percentage overall. An individual licensee, while required to remain consistent with the "canon" source material (TV episodes and films), still needs the freedom to create their product such that it has the greatest possible appeal to their target audience, without being hamstrung by something somebody wrote in a novel that a minor percentage of their potential customers may have read. The same goes for novels and the comics, which are read by a very small number of people who watch the TV series or the films.
As much as I can appreciate the internal consistency the novels have worked for over the past decade+ or so, something I've come to believe in recent years is that Star Trek, like other properties such as Marvel or DC superheroes to name two prominent examples, can exist with versions and variations which don't necessarily reconcile with each other. I don't need for it all to fit into one box, continuity-wise. I can watch The Dark Knight on DVD, before reading the latest issue of Batman: The Widening Gyre, and then sit down to watch an episode of Batman: The Brave and the Bold with my daughter, and worry not one bit that each of these versions of Batman is incompatible with the others. I could do the same with Star Trek, enjoying what I like and dismissing whatever doesn't float my boat.
[DennisMiller]Of course, that's just my opinion...I could be wrong.[/DennisMiller]