I'd say go for speed first, but don't completely ignore the thrusters. Speed helps you outrun single enemies, but if the are coming from multiple directions you need thrusters. Here's a helpful hint. Whichever way you're facing when you exit a star system is the way you'll end up pointing in HyperSpace. So if you plan ahead you won't have to waste time turning too much, just set yourself in whatever direction you'r going next. also, use the autopilot in HS, it saves you tons of fuel and time. but b ready to turn it off if enemies appear, since it doesn't notice them.
As for weapons, some people like to make their flagship into a battleship. In that case you need dynamos and enough crew pods to be able to take a beating, since losing the flag ship means game over. Once you get far enough you'll be able to wipe anyone off the map with your flagship, but in the beginning it can be quite tricky. I've always preferred to fight with my fleet. one of the first ships you get ca take out most enemies. But testing/practicing with different ships in SuperMelee is a good way to figure out what goes well against what.
To assist in fighting, you could also take a look at
this guide that is unfortunately, incomplete. It mostly covers player versus player games, but the concepts in the beginning (pillboxing, flanking, gravity whip and so forth) are important in any battle.
