The death of Anakin Solo had great effects on many people. The most notable person who was affected was his older sister Jaina Solo. From the point in the book Star by Star where Anakin died, Jaina had converted to the dark side of the force. She continued to totally embrace the dark side for the next book Dark Journey and is currently trying to bring herself back to the light side. Many Jedi were also affected by the death of Anakin Solo. Over the course of the New Jedi Order books, Anakin had become a hero among the Jedi. He was believed by many to be one of their saviors from their new enemy.
The New Jedi Order has brought a brand new enemy, the Yuuzhan Vong, to the Star Wars universe. It takes away from the war between the New Republic and the Imperial Remnant which had been fighting for decades and made them face an enemy worse than they have ever faced. This enemy has technology that is totally biological. They use their biologically grown weapons to destroy the New Republic. This makes Star Wars characters have to learn to come up with better methods of fighting these ships. Since the characters don't know how to face the Vong, they lose many of the earlier battles to them.
The Yuuzhan Vong hate any form of mechanical devices. They believe that it is blasphemous to use or even touch anything mechanical. When the Vong capture another planet in their conquest of the galaxy, they usually destroy anything and everything that has to do with technology. They also have deep resentment for the people living in the Star Wars galaxy because they use technology and the Vong see that as disrespect for their god.
The Vong are also blank in the force. This means that they have no presence in the force at all. This helps throw in an interesting plot twist because the growing number of Jedi that rely on the force must face an enemy who is devoid of it. They are excellent warriors who have fighting skills close to those of the Jedi and weapon and armor that can withstand the might of the lightsaber.