The best way I think of balancing, is make Covie ships about twice as expensive as human ships, but VASTLY more powerfull. Like a single covie cruiser is capable of taking on, and winning, against three human cruisers. The covies should have that sense of complete power. While in the series the covies not only overpowered the humans, but outnumbered them to. But then you just can't possibly win lol. So I'd rather have power over numbers.
As for covie ships, they should deal IMMENSE damage against human ships, and also have extremely strong shields. Since, while Acolytes suggestions were good, they weren't true to the series. Covie shields were absurdly strong, but not so much in a recharge rate. You could take them completely offline with enough firepower (allthough they'd come back online in like, less then a minute.) Also, it took several MAC rounds to bring down a covie ship.
I also think the MAC gun should be a special ability, just don't make it cost antimatter or anything, simply give it a cooldown. Considering human ships rarely ran out of MAC rounds during combat, but the MAC's did take a while to recharge between shots. Also, one thing I'd LOVE to see, is slipstream. The Covies had pin-point accurate slipstream, while the humans didn't. You could show this ingame by allowing the covies to enter/exit "phase space" much closer to a planet, and also make them exit in MUCH tighter groups (Like all within a few inches of the phase lane).
However the humans have very poor slipstream, so they enter/exit much farther from a planet, also their ships exit in a much wider area. So like, an entire section of the gravity well would be littered with human ships, since they're inaccurate, human ships had to come out of slipstream far from eachother to prevent collisions and whatnot. Those are my ideas for now, glad to see this mods getting under way.
