As I said, my version of things is rather low level. If you want Starbuck to be a better pilot, then there are a number of remedies. First off, bump him up in level. Second, remember that I have given him an ability to trade PP for dice modifiers. Finally, you can give him a straight-forward add to his Combat roil when piloting a Viper. Personally, I though using Combat checks is a perfect way of emulating the jockeying for a firing position in a furball. If you make the roll, you get your shot. If you don't, then either there was no opportunity or you missed.
A score of 16 in combat is actually quite good, hitting 80% of the time with no modifiers. Being able to push a stunt which is beyond the capabilities of your craft 40% of the time is also very good. It's all just a matter of comparison against the others, really, and depends on your game. As I said, the stats are purely conjectural.
Skill system - why not? There are plenty of skill systems out there that can be tagged onto D&D clones. If you find one that works, sing out. Personally, I'm not that enamoured of them. The old BECMI proficiencies system works so long as you restrict it to things that aren't covered by the character classes, in my opinion. After all, if you have a climbing skill based on DEX, then one of the thief's abilities becomes less useful.
If you want more granularity in the designs of fighters - go for it! I just tried to keep them within the RAW as much as possible. If you're interested, I did write a vehicle combat system with notes on vehicle construction a while back (link -
https://docs.google.com/open?id=0B9m0sXWdlPDQZGViZDg5ZWQtYTFjZS00MWFkLWIzOTItNTgxMDRiZTI0ZTNi if you're interested). If you ask, you'll probably find other people's ideas knocking around as well.
I'd like to see your take on things - after all, there is less information on BSG than on ST. I did think of posting some of my ST:TOS ship designs to the appropriate thread, but I didn't think it was worth it for minor differences in things like Power Pile Base or the number of beam batteries.
The more the merrier!