I suppose it really depends on what you want out of your ship. The Particle Beam can be used as a general use weapon and is and effective replacement for heavy rockets. The tractor beam, on the other hand, gives you a great amount of leverage when combating the aliens. People have successfully completed the alien missions in a corvette using it. Personally, I get both. There's a slight bug in the game that you can exploit that will let you run through both the Rebel and Confed storylines. Simply accept the opening mission for one side and then accept the opening mission for the other side before you complete the first one. At that point, you're good to take on either storyline. It sort've feels like cheating but it beats playing through the entire game with two different pilots.
If taking that approach doesn't float your boat, just play with both and decide which you enjoy more. (If you have to, temporarily load a cheat plugin to test them out)
-AJ