So I ran through the four missions that were included. Nothing in skirmisher yet. What you have here is really good. You've managed to actually capture the Freespace feel in this little mod, instead of just slapping a Deimos skin on something like some of the early FS RTS mods I played for Nexus and Homeworld. I haven't hit any bugs of any sort, and the Duel level offered a nice test bed for all the ships. The only suggestion that I would make is that you tone down the damage and firing rate on the Blob turrets, since not only do the capship fights go a little too quickly, they're often over before beams even come into play. Also, I dunno whether or not it's hardcoded, but the damage from capital ship explosions is also pretty devastating. During the Nebula fight the Vasudans killed the Moloch when it was right in the middle of their formation, and all three of them as well as the other two Shivan ships immediately detonated. It was extremely pretty though.
All in all, what you've done is awesome, and I would love for you too keep going, maybe get some Destroyers in there too. Excellent work.