Okay. I've had more than a bit of a play around now, and I've identified a few things that could use fixing.
Either shields are too strong or weapons are too weak. It took forever to kill a Vagyr Scout in the Homeworld 2 battle, and that was after I'd managed to get behind it. I'm thinking it might be shields. It'd probably be better if fighters didn't have any shields at all.
The fighter weapons have a weird burst mechanism that feels really odd. It seems to be built into the gun and doesn't tie in with weapon power usage. Plus, if you stop firing mid-burst and start again, it only fires the remainder of the burst. EG: Out of a 10 shot burst, if you fire 7 shots, the next trigger pull will fire 3 before the delay sets in.
Right now, because of this, weapon power is worthless. What I would recommend is removing the built-in burst on the weapon and have it fire continuously until weapon power runs out, then make it drain your weapon power really fast (and have it regenerate really fast as well). That way, you don't lose a full burst and putting power to weapons makes the bursts longer.
Some of the backgrounds are too bright for Freespace. It's alright in Homeworld but it makes it really hard to see. Taiidan mission, I'm looking at you.
Some other, little things that I would like to see:
The fly-by sounds on the ships can probably be removed.
Repair Corvettes could probably fit the Support Ship role quite nicely.
Could you pop out the wings/guns of the Acolyte a la this image?: http://shipyards.relicnews.com/somtaaw/images/acolyte2.jpg
. I don't mind either way but it looks more menacing that way.
While it is nice to be able to fly the big ships, I would recommend slaving the Ion Beam Frigate's main gun to the fire key instead of treating it as a turret. It heightens the feeling of flying a great big cannon.