The Darkets are tough, but I try to save at least 2-4 missles for that wave. The Zartoth's (sp?) are easy, they are so slow and big, they make easy targets for the Arrow. Just make sure you have some countermeasures left. If you think the Darkets are tough, wait till you get to the Dralthi's... they stink, and by then, im out of fuel, missles, and countermeasures... game over for me.
Some things I do that help me:
Use the slide in the Arrow. I save so much afterburner fuel using that feature. I live and die by that fuel, so that is a huge plus for me. That feature alone is why I love the Arrow over the Hellcat.
Shields. When you start losing your rear shields, put all your energy into it and put all your power into shields. If you are using full guns, just switch to your lasers, you should have enough energy to last quite awhile.
I only ever fire off a missile when going head on with a enemy fighter. I dont bother firing one if im just on his tail.
Save your missiles. I try to wait till at least the 4 Gothri wave to start using missiles.
I generally try to stay on one target till its dead. At the 5 Darket wave though, it gets tough to impossible.
Other than those little things, I play the prologue

! I play it every day when I get home from work. I even set it to the highest difficulty and see how far I can get... and while that is extremely tough, I think that helps me improve my game significantly.