They seem to be good for different types of missions. For example, Maniac works best when he's dogfighting enemy fighters--don't bother sending him after capships since it's more effective to have him keep the fighters busy while you go after the capships yourself. Catscratch on the other hand is more of a bomber pilot--and you'd better keep the fighters off his back while he makes a bombing run. Primate is good all-around--he seems to last longer than any other pilot except Hawk before being forced to bail out, and he'll rack up quite a few kills as well.
Speaking of WC4 wingmates, I always found it odd that in the sneak-past-Ella mission you only get one wingman--considering the scale of the fighting, I would have expected more than just two Intrepid fighters to be launched.