1. By the end of the series, the Jedi were all like, "Eh, the ends justify the means." Retarted. That's not how a Jedi is supposed to think. It goes against almost everything a Jedi is supposed to stand for; separates them from the Sith.
2. They had Jacen Solo, who's a total WUSS, be the hero of the series by reaching "total Force balance." Um, wut? (He later became a Sith named Darth Caedus, and was still a huge wuss; which sort of, y'know, busts the whole "Force balance" thing)
3. (This was my biggest beef BY FAR) They killed Chewie. FUCKING STUPID!!!! Yeah, I get it, there's supposed to be losses and stuff, but you can't do that! Kill off somebody else, like, say, Wedge Antilles; it achieves the same effect without being a huge asshole. 3PO said it best: "Let the Wookie win."
1. Well, for the first part of the war the Jedi sat around with their heads in the sand imitating ostriches while the rest of the galaxy burned. They didn't even go to the rescue of their entire academy class when the praxeum was attacked! Since their method of doing nothing because we're too scared of being wrong got a few trillion killed, there was little else to do but fight back.
But they never thought that the ends justify the means. The entire subplot of Alpha Red raised that question, along with Zonama Sekot. With Alpha Red, they could've annihilated the Vong, but they felt it was wrong. In that situation, they did not choose the ends over the means, no matter the cost. Another example is with Zonama Sekot. They went there only as a last resort, and they didn't even try to pressure Sekot into helping them. They let Sekot decide, because they knew that again, the ends do not justify the means, and that forcing Sekot to end the war might work, it would corrupt Sekot and themselves.
2. Well, Jacen was a massive wuss in the beginning of the Vong War. He was way too critical and self destructive to be of any use. However, Traitor (Matt Stover, best Star Wars author) provided a very intricate and understandable evolution to Jacen's character, and it detailed and showed exactly what happened to Jacen and why it changed him so much, along with his view of the force. (Vergere is NOT a sith. God, why are many people so thick, especially authors!?)
3. Yeah, killing Chewie did suck. I always liked him, but his death did have a purpose. The purpose: Anakin. Without Chewie's death, and the resulting phsycological trauma inflicted on Anakin, he would not have become the hero and protagonist he needed to be. He needed the catalyst of Chewie's death in order to set him on the path to recognizing his own power and responsibility.
Oh and they did kill off others too. Borsk, Ganner, Anakin, almost Jacen, Coruscant, multiple species, you name it.
And Legacy of the Force (LoTF, or as some fans call it: LOLWTF?) isn't too good of a character reference. Pretty much every single character in that series acted completely unlike themselves. It was like having a dyslexic ADHD child on meth write a fanfiction. Wait, bad example. All of Karen Travesty's books are fanfiction. The Jacen in LoTF is unlike any Jacen from the Swarm War, the Yuuzhan Vong War, the Corellian Trilogy, the Jedi Knights series; well, any other book that had Jacen in it. It's sad too, because he was such a great character who got raped TO DEATH in LoTF.
End Rant Warning
Star Wars really should have ended with NJO, and every other effort after the end of the series should have been devoted to fleshing out other, less touched on parts of Star Wars.
Come on, it's hard not to read the last few pages of Luceno "The Finisher"'s Unifying Force, and not have such a sense of finality and peace.