I have always enjoyed the EU stories I have read, because up until now, they have offered me the ONLY way to experience the further adventures of the OT heroes I grew up with.
That being said, I can totally understand why they need to do this.
Maybe I'm being too forgiving, but you can't blame them if they throw out all of the NJO stuff. Chewbacca's death, what children the Solo and Skywalker families have, the eventual death of one of the Solo kids, the turn to the dark side of another, the death of Luke's wife, etc....
Those novels start 21 years post ROTJ. If they wanted the ST to be set 20-30 years after ROTJ, you either have to film those novels and embrace that storyline or you have to throw it out. There is no middle ground.
There will be some novels that are included. I would be very surprised if the Zahn Trilogy isn't. Those books were created at a time when there wasn't an EU and have the distinction of having their story, plot, and author scrutinized by George Lucas. (Or so was said at the time) However, the second you say that Luke married someone other than Mara Jade OR that Leia and Han didn't have twin children named Jaina and Jacen, well, guess what that means. And if that is the case, then "oh well".
When it comes to the Star Wars Universe, you really can't make the same analogy to the Marvel/Avengers stuff. The comics themselves all exist in multiple universes, the movies are in their own universe, and if a movie is being produced by someone other than Disney/Marvel Studios, it too is in it's own separate universe. Sure they could take all the post-ROTJ books and comics and say "these exist in Star Wars Galaxy 154825173855271" (sorry, just poking fun at the Marvel Universe numbers) - but why bother?
Going back to the Zahn Trilogy. If it had been the only EU material to come out, then maybe including it would be fine. But what about the Dark a Empire comic books? They have shoe-horned the two of them together, but the reality is that the two of them are supposed to be happening at the same time, and even back in the early 90s many fans who read both were like "huh?" - both have their own merits, but in the end, almost negate each other because conflicts in the two stories.
I think fans of the Star Wars EU need to embrace the change that the a Star Trek EU fans had to face years ago, and that is that if your book/comic/whatever does not fit with a story the television or movie makers want to produce then guess which piece of media loses and becomes a "what if" story. I'll give you a hint, it certainly isn't the one that cost millions of dollars to produce.