I think NJO would work better as a TV show, especially considering it's split in half more than it is split in three. So the first part of the series would be up to Star by Star, ending with Anakin's death, Jacen being captured, and Coruscant falling. Then, the second half of the series covers Dark Journey to Unifying Force. The Jedi doing cool stuff isn't the only reason the series is good in my eyes, the novels portraying the normal part of the war were always just as important. In that sense, I think the series works better as a war drama than a trilogy, especially considering just how many characters there are. I agree with you that Thrawn should be in the background as canon material rather than being adapted, but especially now that the sequel trilogy was a dud I think it would have been far better to not make any more trilogies and leave the saga as is. TV shows, one off movies and other material would have been sufficient.Going back to the Vong, had Disney given me the keys to the kingdom and let me do whatever I wanted, I would have taken the NJO books, thrown them, the table and gone "Number 1: The Thrawn Trilogy happened, and its still canon, and Number 2: We are going to narrow these 19 books down into 3 movies, cherry picking the best stuff to adapt".
Is that the best direction? Probably not, but my way at least solves the following problems that the ST crashed into hard:
1) It gives us a framework for a trilogy. A story with a beginning, middle, and end, and there would have to be some changes, but at least its a starting point.
2) The old characters get to maintain their dignity. Luke is married to Mara and is helps to establish a New Jedi Order, the New Republic is in full swing and Leia helped to establish it (even serving as Head of State at some point), and she and Han raised a happy and healthy family.
3) The Vong are the villains, which solves two problems: 1) You aren't just rehashing the OT with another Empire and 2) It doesn't undo the accomplishments achieved in Return of the Jedi. It is a new threat entirely, and they can even toy with the idea that The Emperor and Thrawn both knew the Vong were coming and saw the Empire was the best way to secure the galaxy, and the Republic now has to affirm that their way is the right way.
4) You get a main female character in Jaina Solo who isn't invincible god-lady that knows how to do everything. She is trained by Luke and a student of the academy, and in these books, she struggles with her own anger and potential descent into the Dark Side as the Vong takes more and more away from her. She overcomes this and helps to save the Galaxy with her brother Jacen and Luke working together to do it.
5) Oh and you still get the Empire imagery as what's left of them actually join forces with the Republic. That's right motherfucker! Storm Troopers and TIE Fighters come to the rescue in these books! I would have killed to see Grand Admiral Pellaeon and Admiral Ackbar in a war room together discussing strategy. So you get the nostalgia points for all of that, but you do something different with it to keep it fresh.
So I guess you could say my motives for selecting the NJO as a basis for the ST is purely lazy, or choosing a path of least resistance as its the easiest way to get around any issues people might have, but fuck! I'll still take this over what we ended up getting.