Does class matter in space PvP?
 

Looking at the skill trees, I notice that each class has one tree specific to them and that all the skills in this tree are Ground-Only. So what difference does class make in space combat?

I have been wondering this as well. I know that there are some class-only skills, for example, my science officer has Sensor Sweep. I would guess that these kinds of skills, of which you may have 4 or 5, are the main difference. If there is a difference in damage output, I do not know of it. Perhaps someone with more knowledge can post.

I don't think it matters that much.. people of all 3 can become Captain or Admiral, and command a ship or a fleet.

Of course it matters... I always fly with class...:cool:

nicely done sir.. nicely done.

To actually answer the asked question at Lt. Level 8 and every 10 levels thereafter you get an ability that can quite drasticly impact game play. A list of these player abilities can be found here:
http://sto-intel.org/wiki/Player_Abilities

For example in OB my engineer had Rotate shield frequencies and it saved my nacelles a few times...

I love that phrase. "Saved my nacelles..." I'm gonna have to use that. :P