Well to add to all the comments bout the NJO era. The main effect in the plot as been to completely change the "old hat" that SW novels have ALWAYS had. That being the good guys ALWAYS win. EVERY other series before you got half way through you basically knew what they'd have to do to "win the day".
And actually the Vong have last a few battles b4 Dark Journey. Just not many. But that's the point. There's a complete difference with this enemy. The NR knows NOTHING about them from the start. With the emps they at least new basic drives and fears.
As far as ligthsabers effecting Vong armor. :
1: Lightsabers have never been able to cut ANYthing. Cortis ore, saber hits that and Pfft fizzel, deactivated.
2: Sabers CAN slice vong armor, at its weak points. The NJO era Jedi have never had to deal with 'aiming' a swing, it's always been just make contact ANYwhere on the opponant and cut something.
As far as the Force and the vong. It would nearly cripple a jedi in saber combat because use of a saber relies heavily on the ablity to predict an enemy's next move. And the vong's lack of being within the force actually makes

of since, being a race from a completely new galaxy itself and not just some far off corner of the current galaxy.
As for fleet resources:
1: The NR still HAD a sizeable fleet at the time of Vector Prime. The reason they don't by Dark Journey is simple, they never committed the full fleet in a battle. Thousands of smaller engagments slowly destroyed the majority of the fleet.
Bout Luke. He's been through

of changes of heart and mind since the trilogy. He's tried to live by the old code (that much which he's learned) and NOT use the force for attack. True that may be a flawed logic, if you think about it he's misunderstanding for several reasons:
After the first attack in a war, you're fighting a defense. Sith war, thousands of Jedi ATTACKED Exan Kun's fleet and last base on Yavin. But this was after the Sith first assualted the known galaxy. But Luke hardly has many records of Jedi history.
Also,..the jedi code has never before had to deal with anything remotely close the the Vong invasion. I think even Yoda would make a few changes by now.