I finished reading through the NJO series again, and it allowed me to see some of the flaws that time had wiped from my memory and left only the highlights. As you would imagine from a series with a lot of different writers the characters can have different personalities depending on who is writing them. Jaina Solo is the character who suffers from this the most in the books, although its more of her fluctuating back and forth as if the writers didn't really let each other know how they were developing her. She goes from being certain she's going to die and accepting of that fact, to wanting a future, and back to wanting to die again. It's annoying as a reader for a character to lose the development that she has made.
My biggest complaint is going to come with the Force Heretic trilogy which isn't poorly written, but doesn't much deal with the main crux of the story of the Yuuzhan Vong invading the galaxy. The major characters are split up. Han, Leia, Jaina, Tahiri, and Jagged Fel go to repair communication outposts and relive some older Star Wars books when they return to the planets near the Yvetha crisis and then to Bakura to fight the Ssi-Ruuk. Nominally the Vong are riling up old factional conflicts, but it really just seems like a chance to take a trip down memory lane for no real reason. The third book gives them a new story where they save a communication base while teaming up with some Imperials led by Grand Admiral Palleon, a character who changes a lot depending on the author. The other half of these books are made up by the team of Luke, Mara, Jacen, Danni, and Saba looking for Zonoma Sekot. In the first two books they go to Imperial space and Chiss space and have misunderstandings before redeeming themselves with victories. The third book has them finding Sekot which then becomes much like Rogue Planet in a way that is not particularly endearing.
The two defining problems of the series in my mind are the failure to make the new, non-movie characters matter, and the abrupt ending.
Establishing the new characters was the point of the series and there are books that focus on the new characters and try to establish them, but they are quickly cut off by the returns of Luke, Leia, and Han. Star By Stary is one of the books that works well with this theme and seemed to be the point where Luke said the new Jedi had to solve problems so a team of them go off to Myrkr to kill the Voxyn and we are essentially given a squadron worth of characters to care about, the number of people that worked for the X-Wing novels that didn't worry about the big names. This book is also where they establish the idea that anybody could die when they kill Anakin Skywalker who has been set up as the hero of the series. After this Jaina and Jacen each get their own books which both have issues. Jaina's book Dark Journey has her touch the dark side too quickly, and glazes over that aspect too easily. T'he way she treats Jag and Kyp is a little weird to me as well, but it's a strong showing for the series. Jacen's book Traitor starts too slowly and is a little too philosophical in the soft way that Star Wars books like to delve into philosophy, but the end of this book is phenomenal with the sacrifice that Ganner Rhysode makes, and really vindicates the character who was shallow throughout the series. The problem with these new characters is that these books Jacen and Jaina can't escape the shadows of Luke, Han, and Leia. Jaina is particularly boxed into that as they continually relate her relationship with Jag to that of Han and Leia for some reason that doesn't make any sense to me at all.
Star by Star doesn't just focus on the mission of the New Jedi Order though, it deals with the Vong attack on Coruscant and some stuff with Han and Leia as well which I think could have been cut and helped the book, but the idea is that at the end Coruscant is lost and the New Republic is on the retreat and that's the halfway point of the series. The ending that shows up in the series comes out of nowhere and they ignore a lot of what the New Republic does to weaken the Vong leading up to the last books so they can focus on outlying missions which I think was a poor choice. This series would have been an excellent place to write a new X-Wing series with the new Rogue Squadron led by Gavin Darklighter. However the books don't want to deal with the common soldiers, except in the case of Aaron Allston's books which deal with the defense of one planet and a real military conflict and not the magic missions that the Jedi go on to cause massive damage with small numbers. This is a glaring issue with later books and Jaina's Twin Sun Squadron where lots of the pilots are killed, but never the Jedi who have names, and the dead pilots are only referred to by numbers and their losses mean nothing to the reader.
The series has a lot of highlights to it, but as a whole it's not a shining example of what the Star Wars Expanded Universe can be. For that I'd stick to the Allston X-Wing series books, as well as Shatterpoint. The idea was a good one, but the execution wasn't there.