So in the 90s Trek books to had play with their toys and then put everything back in the box like they found it, while the Star Wars EU was free to do basically whatever they wanted because post-RotJ was never going to be explored in the films.
Now the sequel trilogy is going to invalidate a vast swath of the EU, and future tie ins will have to tread lightly to avoid being contradicted in a future film. At the same time post-Nemesis Star Trek is a free for all that will almost certainly never be contradicted by future canon. And the movie producers are working to make sure all their tie-ins are in continuity with the films, basically mimicking the effect of the claimed 'official-ness' of the old Star Wars EU.
I know the details aren't exactly the same, and that I'm simplifying to suit my comparison, but basically the tie-in continuity situations of Trek/Wars have now switched places!