I agree with this idea, and think specific utility abilities given to individual ships would be neato. Like, the Apogee using a long range scan with its superior !!SCIENCE!!, the Atlas providing shields for nearby fighters, the Conquest getting a MAC cannon in the middle... stuff like that. Whether or not something like superweapons is planned with the future addition of exploration and artifacts (assuming the stuff on the main website is still giving a reasonable picture of future plans) has yet to be seen, but an enterprising modder could probably get in it already (and it seems some already have, to an extent!). Giving a bit more unique flavor to some of the ships, rather than just flat stuff like speed, weapon mounts, and OP points, is always a good thing as far as I'm concerned, so long as it's balanced.