Here is some non-spoiler advice: there are two types of star ships which are by far plain superior to anything else you will get. One can easily destroy a Dreadnought or a Marauder and the other can destroy every other type of ship. They are the Eluder and the Terminator. I won't tell you which races give them, but they are the MOST powerful ships in the game by far, in my opinion (I haven't used the Avatar yet.)
The Eluder is nice, but in my experience, nothing beats the Juggers for defeating the Urquan on the final mission. They're especially good against the AI controlled Kor Ah. Just fly straight up to them and tank their weapons with your shield while holding down the fire button. It could be that I just suck with the other ships, but they were far more effective than anything else I tried.